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Yang N, Liu M, Han J, Jiang M, Zeng Y, Liu Y, Xiang H, Zheng Y. Rational engineering of Halomonas salifodinae to enhance hydroxyectoine production under lower-salt conditions. Appl Microbiol Biotechnol 2024; 108:353. [PMID: 38819481 PMCID: PMC11142988 DOI: 10.1007/s00253-024-13197-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/01/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
Hydroxyectoine is an important compatible solute that holds potential for development into a high-value chemical with broad applications. However, the traditional high-salt fermentation for hydroxyectoine production presents challenges in treating the high-salt wastewater. Here, we report the rational engineering of Halomonas salifodinae to improve the bioproduction of hydroxyectoine under lower-salt conditions. The comparative transcriptomic analysis suggested that the increased expression of ectD gene encoding ectoine hydroxylase (EctD) and the decreased expressions of genes responsible for tricarboxylic acid (TCA) cycle contributed to the increased hydroxyectoine production in H. salifodinae IM328 grown under high-salt conditions. By blocking the degradation pathway of ectoine and hydroxyectoine, enhancing the expression of ectD, and increasing the supply of 2-oxoglutarate, the engineered H. salifodinae strain HS328-YNP15 (ΔdoeA::PUP119-ectD p-gdh) produced 8.3-fold higher hydroxyectoine production than the wild-type strain and finally achieved a hydroxyectoine titer of 4.9 g/L in fed-batch fermentation without any detailed process optimization. This study shows the potential to integrate hydroxyectoine production into open unsterile fermentation process that operates under low-salinity and high-alkalinity conditions, paving the way for next-generation industrial biotechnology. KEY POINTS: • Hydroxyectoine production in H. salifodinae correlates with the salinity of medium • Transcriptomic analysis reveals the limiting factors for hydroxyectoine production • The engineered strain produced 8.3-fold more hydroxyectoine than the wild type.
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Affiliation(s)
- Niping Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- School of Life Sciences, Hebei University, Baoding, 071002, China
| | - Mengshuang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Mingyue Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Zeng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
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2
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Jungmann L, Hoffmann SL, Lang C, De Agazio R, Becker J, Kohlstedt M, Wittmann C. High-efficiency production of 5-hydroxyectoine using metabolically engineered Corynebacterium glutamicum. Microb Cell Fact 2022; 21:274. [PMID: 36578077 PMCID: PMC9798599 DOI: 10.1186/s12934-022-02003-z] [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: 09/27/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Extremolytes enable microbes to withstand even the most extreme conditions in nature. Due to their unique protective properties, the small organic molecules, more and more, become high-value active ingredients for the cosmetics and the pharmaceutical industries. While ectoine, the industrial extremolyte flagship, has been successfully commercialized before, an economically viable route to its highly interesting derivative 5-hydroxyectoine (hydroxyectoine) is not existing. RESULTS Here, we demonstrate high-level hydroxyectoine production, using metabolically engineered strains of C. glutamicum that express a codon-optimized, heterologous ectD gene, encoding for ectoine hydroxylase, to convert supplemented ectoine in the presence of sucrose as growth substrate into the desired derivative. Fourteen out of sixteen codon-optimized ectD variants from phylogenetically diverse bacterial and archaeal donors enabled hydroxyectoine production, showing the strategy to work almost regardless of the origin of the gene. The genes from Pseudomonas stutzeri (PST) and Mycobacterium smegmatis (MSM) worked best and enabled hydroxyectoine production up to 97% yield. Metabolic analyses revealed high enrichment of the ectoines inside the cells, which, inter alia, reduced the synthesis of other compatible solutes, including proline and trehalose. After further optimization, C. glutamicum Ptuf ectDPST achieved a titre of 74 g L-1 hydroxyectoine at 70% selectivity within 12 h, using a simple batch process. In a two-step procedure, hydroxyectoine production from ectoine, previously synthesized fermentatively with C. glutamicum ectABCopt, was successfully achieved without intermediate purification. CONCLUSIONS C. glutamicum is a well-known and industrially proven host, allowing the synthesis of commercial products with granted GRAS status, a great benefit for a safe production of hydroxyectoine as active ingredient for cosmetic and pharmaceutical applications. Because ectoine is already available at commercial scale, its use as precursor appears straightforward. In the future, two-step processes might provide hydroxyectoine de novo from sugar.
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Affiliation(s)
- Lukas Jungmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sarah Lisa Hoffmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Caroline Lang
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Raphaela De Agazio
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Judith Becker
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
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3
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Mantas MJQ, Nunn PB, Ke Z, Codd GA, Barker D. Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB). PHYTOCHEMISTRY 2021; 192:112953. [PMID: 34598041 DOI: 10.1016/j.phytochem.2021.112953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacteria are an ancient clade of photosynthetic prokaryotes, whose worldwide occurrence, especially in water, presents health hazards to humans and animals due to the production of a range of toxins (cyanotoxins). These include the sometimes co-occurring, non-encoded diaminoacid neurotoxins 2,4-diaminobutanoic acid (2,4-DAB) and its structural analogue β-N-methylaminoalanine (BMAA). Knowledge of the biosynthetic pathway for 2,4-DAB, and its role in cyanobacteria, is lacking. The aspartate 4-phosphate pathway is a known route of 2,4-DAB biosynthesis in other bacteria and in some plant species. Another pathway to 2,4-DAB has been described in Lathyrus species. Here, we use bioinformatics analyses to investigate hypotheses concerning 2,4-DAB biosynthesis in cyanobacteria. We assessed the presence or absence of each enzyme in candidate biosynthesis routes, the aspartate 4-phosphate pathway and a pathway to 2,4-DAB derived from S-adenosyl-L-methionine (SAM), in 130 cyanobacterial genomes using sequence alignment, profile hidden Markov models, substrate specificity/active site identification and the reconstruction of gene phylogenies. In the aspartate 4-phosphate pathway, for the 18 species encoding diaminobutanoate-2-oxo-glutarate transaminase, the co-localisation of genes encoding the transaminase with the downstream decarboxylase or ectoine synthase - often within hybrid non-ribosomal peptide synthetase (NRPS)-polyketide synthases (PKS) clusters, NRPS-independent siderophore (NIS) clusters and incomplete ectoine clusters - is compatible with the hypothesis that some cyanobacteria use the aspartate 4-phosphate pathway for 2,4-DAB production. Through this route, in cyanobacteria, 2,4-DAB may be functionally associated with environmental iron-scavenging, via the production of siderophores of the schizokinen/synechobactin type and of some polyamines. In the pathway to 2,4-DAB derived from SAM, eight cyanobacterial species encode homologs of SAM-dependent 3-amino-3-carboxypropyl transferases. Other enzymes in this pathway have not yet been purified or sequenced. Ultimately, the biosynthesis of 2,4-DAB appears to be either restricted to some cyanobacterial species, or there may be multiple and additional routes, and roles, for the synthesis of this neurotoxin.
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Affiliation(s)
- Maria José Q Mantas
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, The King's Buildings, Edinburgh, EH9 3FL, United Kingdom.
| | - Peter B Nunn
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom.
| | - Ziying Ke
- School of Biological Sciences, Roger Land Building, The King's Buildings, Alexander Crum Brown Road, Edinburgh, EH9 3FF, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.
| | - Geoffrey A Codd
- School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom; School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom.
| | - Daniel Barker
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, The King's Buildings, Edinburgh, EH9 3FL, United Kingdom.
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4
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Flachbart LK, Gertzen CGW, Gohlke H, Marienhagen J. Development of a Biosensor Platform for Phenolic Compounds Using a Transition Ligand Strategy. ACS Synth Biol 2021; 10:2002-2014. [PMID: 34369151 DOI: 10.1021/acssynbio.1c00165] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The time-consuming and laborious characterization of protein or microbial strain designs limits the development of high-performance biocatalysts for biotechnological applications. Here, transcriptional biosensors emerged as valuable tools as they allow for rapid characterization of several thousand variants within a very short time. However, for many molecules of interest, no specific transcriptional regulator determining a biosensor's specificity is available. We present an approach for rapidly engineering biosensor specificities using a semirational transition ligand approach combined with fluorescence-activated cell sorting. In this two-step approach, a biosensor is first evolved toward a more relaxed-ligand specificity before using the resulting variant as the starting point in a second round of directed evolution toward high specificity for several chemically different ligands. By following this strategy, highly specific biosensors for 4-hydroxybenzoic acid, p-coumaric acid, 5-bromoferulic acid, and 6-methyl salicylic acid were developed, starting from a biosensor for the intracellular detection of trans-cinnamic acid.
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Affiliation(s)
- Lion Konstantin Flachbart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Christoph Gerhard Wilhelm Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
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5
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Mulnaes D, Golchin P, Koenig F, Gohlke H. TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning. J Chem Theory Comput 2021; 17:4599-4613. [PMID: 34161735 DOI: 10.1021/acs.jctc.1c00129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein domains are independent, functional, and stable structural units of proteins. Accurate protein domain boundary prediction plays an important role in understanding protein structure and evolution, as well as for protein structure prediction. Current domain boundary prediction methods differ in terms of boundary definition, methodology, and training databases resulting in disparate performance for different proteins. We developed TopDomain, an exhaustive metapredictor, that uses deep neural networks to combine multisource information from sequence- and homology-based features of over 50 primary predictors. For this purpose, we developed a new domain boundary data set termed the TopDomain data set, in which the true annotations are informed by SCOPe annotations, structural domain parsers, human inspection, and deep learning. We benchmark TopDomain against 2484 targets with 3354 boundaries from the TopDomain test set and achieve F1 scores of 78.4% and 73.8% for multidomain boundary prediction within ±20 residues and ±10 residues of the true boundary, respectively. When examined on targets from CASP11-13 competitions, TopDomain achieves F1 scores of 47.5% and 42.8% for multidomain proteins. TopDomain significantly outperforms 15 widely used, state-of-the-art ab initio and homology-based domain boundary predictors. Finally, we implemented TopDomainTMC, which accurately predicts whether domain parsing is necessary for the target protein.
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Affiliation(s)
- Daniel Mulnaes
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Pegah Golchin
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Filip Koenig
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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6
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Hermann L, Mais CN, Czech L, Smits SHJ, Bange G, Bremer E. The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient. Biol Chem 2021; 401:1443-1468. [PMID: 32755967 DOI: 10.1515/hsz-2020-0223] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.
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Affiliation(s)
- Lucas Hermann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Karl-von Frisch Str. 10, D-35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
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7
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Peng J, Zhang Y, Jiang Y, Zhang H. Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References. J Chem Inf Model 2021; 61:2981-2997. [PMID: 34080414 DOI: 10.1021/acs.jcim.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg2+ ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl2 solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case. The feasibility of reproducing more properties of Mg2+ such as diffusion constants and water exchange rates using a nonbonded dummy model is demonstrated. Underestimated activity derivative and osmotic coefficient of MgCl2 solutions in high concentration reveal a necessity for further optimization of ion-pair interactions. The developed dummy models are applicable to metal coordination with Asp, Glu, and His residues in metalloenzymes, and the performance in predicting monodentate or bidentate binding modes of Asp/Glu residues depends on the complexity of metal centers and the choice of protein force fields. When both the binding modes coexist, the nonbonded dummy models outperform point charge models, probably in need of considering polarization of metal-binding residues by, for instance, charge calibration in classical force fields. This work is valuable for the use and further development of magnesium ion models for simulations of metal-containing systems with good accuracy.
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Affiliation(s)
- Jiarong Peng
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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8
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Nutschel C, Coscolín C, David B, Mulnaes D, Ferrer M, Jaeger KE, Gohlke H. Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones. J Chem Inf Model 2021; 61:2383-2395. [PMID: 33949194 DOI: 10.1021/acs.jcim.1c00152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Understanding mechanisms of promiscuity is increasingly important from a fundamental and application point of view. As to enzyme structural dynamics, more promiscuous enzymes generally have been recognized to also be more flexible. However, examples for the opposite received much less attention. Here, we exploit comprehensive experimental information on the substrate promiscuity of 147 esterases tested against 96 esters together with computationally efficient rigidity analyses to understand the molecular origin of the observed promiscuity range. Unexpectedly, our data reveal that promiscuous esterases are significantly less flexible than specific ones, are significantly more thermostable, and have a significantly increased specific activity. These results may be reconciled with a model according to which structural flexibility in the case of specific esterases serves for conformational proofreading. Our results signify that an esterase sequence space can be screened by rigidity analyses for promiscuous esterases as starting points for further exploration in biotechnology and synthetic chemistry.
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Affiliation(s)
- Christina Nutschel
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Benoit David
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Daniel Mulnaes
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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9
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Mulnaes D, Koenig F, Gohlke H. TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction. J Chem Inf Model 2021; 61:548-553. [PMID: 33464891 DOI: 10.1021/acs.jcim.0c01202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins carry out the most fundamental processes of life such as cellular metabolism, regulation, and communication. Understanding these processes at a molecular level requires knowledge of their three-dimensional structures. Experimental techniques such as X-ray crystallography, NMR spectroscopy, and cryogenic electron microscopy can resolve protein structures but are costly and time-consuming and do not work for all proteins. Computational protein structure prediction tries to overcome these problems by predicting the structure of a new protein using existing protein structures as a resource. Here we present TopSuite, a web server for protein model quality assessment (TopScore) and template-based protein structure prediction (TopModel). TopScore provides meta-predictions for global and residue-wise model quality estimation using deep neural networks. TopModel predicts protein structures using a top-down consensus approach to aid the template selection and subsequently uses TopScore to refine and assess the predicted structures. The TopSuite Web server is freely available at https://cpclab.uni-duesseldorf.de/topsuite/.
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Affiliation(s)
- Daniel Mulnaes
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Filip Koenig
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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10
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Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins. Nat Commun 2020; 11:1725. [PMID: 32265442 PMCID: PMC7138851 DOI: 10.1038/s41467-020-15441-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/04/2020] [Indexed: 11/08/2022] Open
Abstract
Class I glutaredoxins are enzymatically active, glutathione-dependent oxidoreductases, whilst class II glutaredoxins are typically enzymatically inactive, Fe-S cluster-binding proteins. Enzymatically active glutaredoxins harbor both a glutathione-scaffold site for reacting with glutathionylated disulfide substrates and a glutathione-activator site for reacting with reduced glutathione. Here, using yeast ScGrx7 as a model protein, we comprehensively identified and characterized key residues from four distinct protein regions, as well as the covalently bound glutathione moiety, and quantified their contribution to both interaction sites. Additionally, we developed a redox-sensitive GFP2-based assay, which allowed the real-time assessment of glutaredoxin structure-function relationships inside living cells. Finally, we employed this assay to rapidly screen multiple glutaredoxin mutants, ultimately enabling us to convert enzymatically active and inactive glutaredoxins into each other. In summary, we have gained a comprehensive understanding of the mechanistic underpinnings of glutaredoxin catalysis and have elucidated the determinant structural differences between the two main classes of glutaredoxins. Glutaredoxins play a central role in numerous biological processes including cellular redox homeostasis and Fe-S cluster biogenesis. Here the authors establish the molecular basis for glutaredoxin redox catalysis through comprehensive biochemical and structural analyses.
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11
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Richter AA, Kobus S, Czech L, Hoeppner A, Zarzycki J, Erb TJ, Lauterbach L, Dickschat JS, Bremer E, Smits SHJ. The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine. J Biol Chem 2020; 295:2822-2838. [PMID: 31969391 DOI: 10.1074/jbc.ra119.011277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/19/2020] [Indexed: 12/17/2022] Open
Abstract
Ectoine is a solute compatible with the physiologies of both prokaryotic and eukaryotic cells and is widely synthesized by bacteria as an osmotic stress protectant. Because it preserves functional attributes of proteins and macromolecular complexes, it is considered a chemical chaperone and has found numerous practical applications. However, the mechanism of its biosynthesis is incompletely understood. The second step in ectoine biosynthesis is catalyzed by l-2,4-diaminobutyrate acetyltransferase (EctA; EC 2.3.1.178), which transfers the acetyl group from acetyl-CoA to EctB-formed l-2,4-diaminobutyrate (DAB), yielding N-γ-acetyl-l-2,4-diaminobutyrate (N-γ-ADABA), the substrate of ectoine synthase (EctC). Here, we report the biochemical and structural characterization of the EctA enzyme from the thermotolerant bacterium Paenibacillus lautus (Pl). We found that (Pl)EctA forms a homodimer whose enzyme activity is highly regiospecific by producing N-γ-ADABA but not the ectoine catabolic intermediate N-α-acetyl-l-2,4-diaminobutyric acid. High-resolution crystal structures of (Pl)EctA (at 1.2-2.2 Å resolution) (i) for its apo-form, (ii) in complex with CoA, (iii) in complex with DAB, (iv) in complex with both CoA and DAB, and (v) in the presence of the product N-γ-ADABA were obtained. To pinpoint residues involved in DAB binding, we probed the structure-function relationship of (Pl)EctA by site-directed mutagenesis. Phylogenomics shows that EctA-type proteins from both Bacteria and Archaea are evolutionarily highly conserved, including catalytically important residues. Collectively, our biochemical and structural findings yielded detailed insights into the catalytic core of the EctA enzyme that laid the foundation for unraveling its reaction mechanism.
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Affiliation(s)
- Alexandra A Richter
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany; Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Lukas Lauterbach
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany; Institute of Biochemistry, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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12
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Mulnaes D, Porta N, Clemens R, Apanasenko I, Reiners J, Gremer L, Neudecker P, Smits SHJ, Gohlke H. TopModel: Template-Based Protein Structure Prediction at Low Sequence Identity Using Top-Down Consensus and Deep Neural Networks. J Chem Theory Comput 2020; 16:1953-1967. [DOI: 10.1021/acs.jctc.9b00825] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Daniel Mulnaes
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicola Porta
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Rebecca Clemens
- Institute für Biochemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Irina Apanasenko
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & JuStruct, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Jens Reiners
- Institute für Biochemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Center for Structural Studies Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Lothar Gremer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & JuStruct, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Philipp Neudecker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & JuStruct, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sander H. J. Smits
- Institute für Biochemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Center for Structural Studies Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & JuStruct, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- John von Neumann Institute for Computing (NIC) & Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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13
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Richter AA, Mais CN, Czech L, Geyer K, Hoeppner A, Smits SHJ, Erb TJ, Bange G, Bremer E. Biosynthesis of the Stress-Protectant and Chemical Chaperon Ectoine: Biochemistry of the Transaminase EctB. Front Microbiol 2019; 10:2811. [PMID: 31921013 PMCID: PMC6915088 DOI: 10.3389/fmicb.2019.02811] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteria frequently adapt to high osmolarity surroundings through the accumulation of compatible solutes. Ectoine is a prominent member of these types of stress protectants and is produced via an evolutionarily conserved biosynthetic pathway beginning with the L-2,4-diaminobutyrate (DAB) transaminase (TA) EctB. Here, we studied EctB from the thermo-tolerant Gram-positive bacterium Paenibacillus lautus (Pl) and show that this tetrameric enzyme is highly tolerant to salt, pH, and temperature. During ectoine biosynthesis, EctB converts L-glutamate and L-aspartate-beta-semialdehyde into 2-oxoglutarate and DAB, but it also catalyzes the reverse reaction. Our analysis unravels that EctB enzymes are mechanistically identical to the PLP-dependent gamma-aminobutyrate TAs (GABA-TAs) and only differ with respect to substrate binding. Inspection of the genomic context of the ectB gene in P. lautus identifies an unusual arrangement of juxtapositioned genes for ectoine biosynthesis and import via an Ehu-type binding-protein-dependent ABC transporter. This operon-like structure suggests the operation of a highly coordinated system for ectoine synthesis and import to maintain physiologically adequate cellular ectoine pools under osmotic stress conditions in a resource-efficient manner. Taken together, our study provides an in-depth mechanistic and physiological description of EctB, the first enzyme of the ectoine biosynthetic pathway.
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Affiliation(s)
- Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Christopher-Nils Mais
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Kyra Geyer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gert Bange
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
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14
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Mustakhimov II, Reshetnikov AS, But SY, Rozova ON, Khmelenina VN, Trotsenko YA. Engineering of Hydroxyectoine Production based on the Methylomicrobium alcaliphilum. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819130015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Czech L, Wilcken S, Czech O, Linne U, Brauner J, Smits SHJ, Galinski EA, Bremer E. Exploiting Substrate Promiscuity of Ectoine Hydroxylase for Regio- and Stereoselective Modification of Homoectoine. Front Microbiol 2019; 10:2745. [PMID: 31827466 PMCID: PMC6890836 DOI: 10.3389/fmicb.2019.02745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Extant enzymes are not only highly efficient biocatalysts for a single, or a group of chemically closely related substrates but often have retained, as a mark of their evolutionary history, a certain degree of substrate ambiguity. We have exploited the substrate ambiguity of the ectoine hydroxylase (EctD), a member of the non-heme Fe(II)-containing and 2-oxoglutarate-dependent dioxygenase superfamily, for such a task. Naturally, the EctD enzyme performs a precise regio- and stereoselective hydroxylation of the ubiquitous stress protectant and chemical chaperone ectoine (possessing a six-membered pyrimidine ring structure) to yield trans-5-hydroxyectoine. Using a synthetic ectoine derivative, homoectoine, which possesses an expanded seven-membered diazepine ring structure, we were able to selectively generate, both in vitro and in vivo, trans-5-hydroxyhomoectoine. For this transformation, we specifically used the EctD enzyme from Pseudomonas stutzeri in a whole cell biocatalyst approach, as this enzyme exhibits high catalytic efficiency not only for its natural substrate ectoine but also for homoectoine. Molecular docking approaches with the crystal structure of the Sphingopyxis alaskensis EctD protein predicted the formation of trans-5-hydroxyhomoectoine, a stereochemical configuration that we experimentally verified by nuclear-magnetic resonance spectroscopy. An Escherichia coli cell factory expressing the P. stutzeri ectD gene from a synthetic promoter imported homoectoine via the ProU and ProP compatible solute transporters, hydroxylated it, and secreted the formed trans-5-hydroxyhomoectoine, independent from all currently known mechanosensitive channels, into the growth medium from which it could be purified by high-pressure liquid chromatography.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Sarah Wilcken
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Oliver Czech
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Jarryd Brauner
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Erwin A Galinski
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-Universität Marburg, Marburg, Germany
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16
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Chen WC, Hsu CC, Wang LF, Lan JCW, Chang YK, Wei YH. Exploring useful fermentation strategies for the production of hydroxyectoine with a halophilic strain, Halomonas salina BCRC 17875. J Biosci Bioeng 2019; 128:332-336. [PMID: 30935782 DOI: 10.1016/j.jbiosc.2019.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/15/2019] [Accepted: 02/26/2019] [Indexed: 01/22/2023]
Abstract
Hydroxyectoine, an ectoine derivative, is the most common compatible solute in halophilic microorganisms for resisting harsh environments. Compatible solutes can be utilized in fields such as cosmetics, medicine, and biochemistry. Moderately halophilic microorganisms produce much less hydroxyectoine as compared with ectoine. In this study, we first evaluate the effect of medium formulation (i.e., yeast extract (YE) medium and high yeast extract (HYE) medium) on hydroxyectoine production. In addition, an investigation of hydroxyectoine production by Halomonas salina under optimal conditions for vital factors (i.e., iron and α-ketoglutarate) and hydroxylase activity was also carried out. As a result, hydroxyectoine production was obviously elevated (0.9 g/L to 1.8 g/L) when the HYE medium was utilized. Furthermore, hydroxyectoine production further increased to 2.4 g/L when both the α-ketoglutarate and iron factors were added to the HYE medium in the early stationary phase. In addition, we found that ectoine hydroxylase activity increased more when a combination of iron and α-ketoglutarate was used than when either was used alone. The results showed that the alteration of iron and α-ketoglutarate clearly stimulated the expression of ectoine hydroxylase, which in turn affected hydroxyectoine synthesis. This study also showed that hydroxyectoine production was further raised from 2.4 g/L to 2.9 g/L when 50 mM of α-ketoglutarate and 1 mM of iron were added to the HYE medium. Ultimately, the experimental results showed using the optimal conditions further elevated the hydroxyectoine production yield to 2.90 g/L, which was over 3-fold higher than the best results obtained from the original medium.
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Affiliation(s)
- Wei-Chuan Chen
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, No. 135 Yuan-Tung Rd., Chung-Li Dist., Taoyuan City 32003, Taiwan, ROC
| | - Ching-Cha Hsu
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, No. 135 Yuan-Tung Rd., Chung-Li Dist., Taoyuan City 32003, Taiwan, ROC
| | - Li-Fen Wang
- Department of Applied Chemistry and Materials Science, Fooyin University, No. 151 Jinxue Rd., Daliao Dist., Kaohsiung City 83102, Taiwan, ROC
| | - John Chi-Wei Lan
- Department of Chemical Engineering and Materials Science, Yuan Ze University, No. 135 Yuan-Tung Rd., Chung-Li Dist., Taoyuan City 32003, Taiwan, ROC
| | - Yu-Kaung Chang
- Department & Graduate Institute of Chemical Engineering, Ming Chi University of Technology, No. 84 Gungjuan Rd., Taishan Dist., New Taipei City 24301, Taiwan, ROC
| | - Yu-Hong Wei
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, No. 135 Yuan-Tung Rd., Chung-Li Dist., Taoyuan City 32003, Taiwan, ROC.
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17
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Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis. Sci Rep 2019; 9:364. [PMID: 30674920 PMCID: PMC6344544 DOI: 10.1038/s41598-018-36247-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022] Open
Abstract
Ectoine synthase (EctC) is the signature enzyme for the production of ectoine, a compatible solute and chemical chaperone widely synthesized by bacteria as a cellular defense against the detrimental effects of osmotic stress. EctC catalyzes the last step in ectoine synthesis through cyclo-condensation of the EctA-formed substrate N-gamma-acetyl-L-2,4-diaminobutyric acid via a water elimination reaction. We have biochemically and structurally characterized the EctC enzyme from the thermo-tolerant bacterium Paenibacillus lautus (Pl). EctC is a member of the cupin superfamily and forms dimers, both in solution and in crystals. We obtained high-resolution crystal structures of the (Pl)EctC protein in forms that contain (i) the catalytically important iron, (ii) iron and the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid, and (iii) iron and the enzyme reaction product ectoine. These crystal structures lay the framework for a proposal for the EctC-mediated water-elimination reaction mechanism. Residues involved in coordinating the metal, the substrate, or the product within the active site of ectoine synthase are highly conserved among a large group of EctC-type proteins. Collectively, the biochemical, mutational, and structural data reported here yielded detailed insight into the structure-function relationship of the (Pl)EctC enzyme and are relevant for a deeper understanding of the ectoine synthase family as a whole.
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18
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Directed Evolution of a Homodimeric Laccase from Cerrena unicolor BBP6 by Random Mutagenesis and In Vivo Assembly. Int J Mol Sci 2018; 19:ijms19102989. [PMID: 30274366 PMCID: PMC6213006 DOI: 10.3390/ijms19102989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/19/2018] [Accepted: 09/27/2018] [Indexed: 11/21/2022] Open
Abstract
Laccases have great potential for industrial applications due to their green catalytic properties and broad substrate specificities, and various studies have attempted to improve the catalytic performance of these enzymes. Here, to the best of our knowledge, we firstly report the directed evolution of a homodimeric laccase from Cerrena unicolor BBP6 fused with α-factor prepro-leader that was engineered through random mutagenesis followed by in vivo assembly in Saccharomyces cerevisiae. Three evolved fusion variants selected from ~3500 clones presented 31- to 37-fold increases in total laccase activity, with better thermostability and broader pH profiles. The evolved α-factor prepro-leader enhanced laccase expression levels by up to 2.4-fold. Protein model analysis of these variants reveals that the beneficial mutations have influences on protein pKa shift, subunit interaction, substrate entrance, and C-terminal function.
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19
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Mulnaes D, Gohlke H. TopScore: Using Deep Neural Networks and Large Diverse Data Sets for Accurate Protein Model Quality Assessment. J Chem Theory Comput 2018; 14:6117-6126. [DOI: 10.1021/acs.jctc.8b00690] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Daniel Mulnaes
- Department of Mathematics and Natural Sciences, Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Department of Mathematics and Natural Sciences, Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- John von Neumann
Institute for Computing (NIC), Jülich Supercomputing Centre
(JSC) & Institute for Complex Systems - Structural Biochemistry
(ICS 6), Forschungszentrum Jülich GmbH, Jülich, Germany
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20
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Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. Nat Commun 2018; 9:2114. [PMID: 29844506 PMCID: PMC5974017 DOI: 10.1038/s41467-018-04513-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/04/2018] [Indexed: 11/09/2022] Open
Abstract
Glutarate is a five carbon platform chemical produced during the catabolism of L-lysine. It is known that it can be catabolized through the glutaryl-CoA dehydrogenation pathway. Here, we discover that Pseudomonas putida KT2440 has an additional glutarate catabolic pathway involving L-2-hydroxyglutarate (L-2-HG), an abnormal metabolite produced from 2-ketoglutarate (2-KG). In this pathway, CsiD, a Fe2+/2-KG-dependent glutarate hydroxylase, is capable of converting glutarate into L-2-HG, and LhgO, an L-2-HG oxidase, can catalyze L-2-HG into 2-KG. We construct a recombinant strain that lacks both glutarate catabolic pathways. It can produce glutarate from L-lysine with a yield of 0.85 mol glutarate/mol L-lysine. Thus, L-2-HG anabolism and catabolism is a metabolic alternative to the glutaryl-CoA dehydrogenation pathway in P. putida KT2440; L-lysine can be both ketogenic and glucogenic.
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21
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Czech L, Hermann L, Stöveken N, Richter AA, Höppner A, Smits SHJ, Heider J, Bremer E. Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis. Genes (Basel) 2018; 9:genes9040177. [PMID: 29565833 PMCID: PMC5924519 DOI: 10.3390/genes9040177] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/26/2023] Open
Abstract
Fluctuations in environmental osmolarity are ubiquitous stress factors in many natural habitats of microorganisms, as they inevitably trigger osmotically instigated fluxes of water across the semi-permeable cytoplasmic membrane. Under hyperosmotic conditions, many microorganisms fend off the detrimental effects of water efflux and the ensuing dehydration of the cytoplasm and drop in turgor through the accumulation of a restricted class of organic osmolytes, the compatible solutes. Ectoine and its derivative 5-hydroxyectoine are prominent members of these compounds and are synthesized widely by members of the Bacteria and a few Archaea and Eukarya in response to high salinity/osmolarity and/or growth temperature extremes. Ectoines have excellent function-preserving properties, attributes that have led to their description as chemical chaperones and fostered the development of an industrial-scale biotechnological production process for their exploitation in biotechnology, skin care, and medicine. We review, here, the current knowledge on the biochemistry of the ectoine/hydroxyectoine biosynthetic enzymes and the available crystal structures of some of them, explore the genetics of the underlying biosynthetic genes and their transcriptional regulation, and present an extensive phylogenomic analysis of the ectoine/hydroxyectoine biosynthetic genes. In addition, we address the biochemistry, phylogenomics, and genetic regulation for the alternative use of ectoines as nutrients.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Lucas Hermann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Nadine Stöveken
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Astrid Höppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
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22
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Milić D, Dick M, Mulnaes D, Pfleger C, Kinnen A, Gohlke H, Groth G. Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1. Sci Rep 2018; 8:3890. [PMID: 29497085 PMCID: PMC5832771 DOI: 10.1038/s41598-018-21952-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/13/2018] [Indexed: 12/21/2022] Open
Abstract
Synthetic peptides derived from ethylene-insensitive protein 2 (EIN2), a central regulator of ethylene signalling, were recently shown to delay fruit ripening by interrupting protein-protein interactions in the ethylene signalling pathway. Here, we show that the inhibitory peptide NOP-1 binds to the GAF domain of ETR1 - the prototype of the plant ethylene receptor family. Site-directed mutagenesis and computational studies reveal the peptide interaction site and a plausible molecular mechanism for the ripening inhibition.
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Affiliation(s)
- Dalibor Milić
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Markus Dick
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Daniel Mulnaes
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Pfleger
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Kinnen
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Georg Groth
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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23
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Rehberg N, Akone HS, Ioerger TR, Erlenkamp G, Daletos G, Gohlke H, Proksch P, Kalscheuer R. Chlorflavonin Targets Acetohydroxyacid Synthase Catalytic Subunit IlvB1 for Synergistic Killing of Mycobacterium tuberculosis. ACS Infect Dis 2018; 4:123-134. [PMID: 29108416 DOI: 10.1021/acsinfecdis.7b00055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The flavonoid natural compound chlorflavonin was isolated from the endophytic fungus Mucor irregularis, which was obtained from the Cameroonian medicinal plant Moringa stenopetala. Chlorflavonin exhibited strong growth inhibitory activity in vitro against Mycobacterium tuberculosis (MIC90 1.56 μM) while exhibiting no cytotoxicity toward the human cell lines MRC-5 and THP-1 up to concentrations of 100 μM. Mapping of resistance-mediating mutations employing whole-genome sequencing, chemical supplementation assays, and molecular docking studies as well as enzymatic characterization revealed that chlorflavonin specifically inhibits the acetohydroxyacid synthase catalytic subunit IlvB1, causing combined auxotrophies to branched-chain amino acids and to pantothenic acid. While exhibiting a bacteriostatic effect in monotreatment, chlorflavonin displayed synergistic effects with the first-line antibiotic isoniazid and particularly with delamanid, leading to a complete sterilization in liquid culture in combination treatment. Using a fluorescent reporter strain, intracellular activity of chlorflavonin against Mycobacterium tuberculosis inside infected macrophages was demonstrated and was superior to streptomycin treatment.
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Affiliation(s)
- Nidja Rehberg
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Herve Sergi Akone
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Faculty of Science, Department of Chemistry, University of Douala,
PO Box 24157, 2701 Douala, Cameroon
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, 710 Ross St., College Station, Texas 77843, United States
| | - German Erlenkamp
- Institute
of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Georgios Daletos
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute
of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Peter Proksch
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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24
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Schulz A, Stöveken N, Binzen IM, Hoffmann T, Heider J, Bremer E. Feeding on compatible solutes: A substrate-induced pathway for uptake and catabolism of ectoines and its genetic control by EnuR. Environ Microbiol 2016; 19:926-946. [PMID: 27318028 DOI: 10.1111/1462-2920.13414] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/19/2016] [Indexed: 01/19/2023]
Abstract
Ectoine and 5-hydroxyectoine are widely synthesized microbial osmostress protectants. They are also versatile nutrients but their catabolism and the genetic regulation of the corresponding genes are incompletely understood. Using the marine bacterium Ruegeria pomeroyi DSS-3, we investigated the utilization of ectoines and propose a seven steps comprising catabolic route that entails an initial conversion of 5-hydroxyectoine to ectoine, the opening of the ectoine ring, and the subsequent degradation of this intermediate to l-aspartate. The catabolic genes are co-transcribed with three genes encoding a 5-hydroxyectoine/ectoine-specific TRAP transporter. A chromosomal deletion of this entire gene cluster abolishes the utilization of ectoines as carbon and nitrogen sources. The presence of ectoines in the growth medium triggers enhanced expression of the importer and catabolic operon, a process dependent on a substrate-inducible promoter that precedes this gene cluster. EnuR, a member of the MocR/GabR-type transcriptional regulators, controls the activity of this promoter and functions as a repressor. EnuR contains a covalently bound pyridoxal-5'-phosphate, and we suggest that this co-factor is critical for the substrate-mediated induction of the 5-hydroxyectoine/ectoine import and catabolic genes. Bioinformatics showed that ectoine consumers are restricted to the Proteobacteria and that EnuR is likely a central regulator for most ectoine/5-hydroxyectoine catabolic genes.
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Affiliation(s)
- Annina Schulz
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Nadine Stöveken
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
| | - Ina M Binzen
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
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25
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Czech L, Stöveken N, Bremer E. EctD-mediated biotransformation of the chemical chaperone ectoine into hydroxyectoine and its mechanosensitive channel-independent excretion. Microb Cell Fact 2016; 15:126. [PMID: 27439307 PMCID: PMC4955205 DOI: 10.1186/s12934-016-0525-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/12/2016] [Indexed: 11/26/2022] Open
Abstract
Background Ectoine and its derivative 5-hydroxyectoine are cytoprotectants widely synthesized by microorganisms as a defense against the detrimental effects of high osmolarity on cellular physiology and growth. Both ectoines possess the ability to preserve the functionality of proteins, macromolecular complexes, and even entire cells, attributes that led to their description as chemical chaperones. As a consequence, there is growing interest in using ectoines for biotechnological purposes, in skin care, and in medical applications. 5-Hydroxyectoine is synthesized from ectoine through a region- and stereo-specific hydroxylation reaction mediated by the EctD enzyme, a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenases. This chemical modification endows the newly formed 5-hydroxyectoine with either superior or different stress- protecting and stabilizing properties. Microorganisms producing 5-hydroxyectoine typically contain a mixture of both ectoines. We aimed to establish a recombinant microbial cell factory where 5-hydroxyectoine is (i) produced in highly purified form, and (ii) secreted into the growth medium. Results We used an Escherichia coli strain (FF4169) defective in the synthesis of the osmostress protectant trehalose as the chassis for our recombinant cell factory. We expressed in this strain a plasmid-encoded ectD gene from Pseudomonas stutzeri A1501 under the control of the anhydrotetracycline-inducible tet promoter. We chose the ectoine hydroxylase from P. stutzeri A1501 for our cell factory after a careful comparison of the in vivo performance of seven different EctD proteins. In the final set-up of the cell factory, ectoine was provided to salt-stressed cultures of strain FF4169 (pMP41; ectD+). Ectoine was imported into the cells via the osmotically inducible ProP and ProU transport systems, intracellularly converted to 5-hydroxyectoine, which was then almost quantitatively secreted into the growth medium. Experiments with an E. coli mutant lacking all currently known mechanosensitive channels (MscL, MscS, MscK, MscM) revealed that the release of 5-hydroxyectoine under osmotic steady-state conditions occurred independently of these microbial safety valves. In shake-flask experiments, 2.13 g l−1 ectoine (15 mM) was completely converted into 5-hydroxyectoine within 24 h. Conclusions We describe here a recombinant E. coli cell factory for the production and secretion of the chemical chaperone 5-hydroxyectoine free from contaminating ectoine. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0525-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University at Marburg, 35043, Marburg, Germany
| | - Nadine Stöveken
- Laboratory for Microbiology, Department of Biology, Philipps-University at Marburg, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-University Marburg at Marburg, 35043, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University at Marburg, 35043, Marburg, Germany. .,LOEWE Center for Synthetic Microbiology, Philipps-University Marburg at Marburg, 35043, Marburg, Germany. .,Laboratory for Microbiology, Department of Biology, Philipps-University at Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany.
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26
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Zhang Z, Gu Q, Jaguva Vasudevan AA, Hain A, Kloke BP, Hasheminasab S, Mulnaes D, Sato K, Cichutek K, Häussinger D, Bravo IG, Smits SHJ, Gohlke H, Münk C. Determinants of FIV and HIV Vif sensitivity of feline APOBEC3 restriction factors. Retrovirology 2016; 13:46. [PMID: 27368163 PMCID: PMC4930625 DOI: 10.1186/s12977-016-0274-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/09/2016] [Indexed: 02/07/2023] Open
Abstract
Background Feline immunodeficiency virus (FIV) is a global pathogen of Felidae species and a model system for Human immunodeficiency virus (HIV)-induced AIDS. In felids such as the domestic cat (Felis catus), APOBEC3 (A3) genes encode for single-domain A3Z2s, A3Z3 and double-domain A3Z2Z3 anti-viral cytidine deaminases. The feline A3Z2Z3 is expressed following read-through transcription and alternative splicing, introducing a previously untranslated exon in frame, encoding a domain insertion called linker. Only A3Z3 and A3Z2Z3 inhibit Vif-deficient FIV. Feline A3s also are restriction factors for HIV and Simian immunodeficiency viruses (SIV). Surprisingly, HIV-2/SIV Vifs can counteract feline A3Z2Z3. Results To identify residues in feline A3s that Vifs need for interaction and degradation, chimeric human–feline A3s were tested. Here we describe the molecular direct interaction of feline A3s with Vif proteins from cat FIV and present the first structural A3 model locating these interaction regions. In the Z3 domain we have identified residues involved in binding of FIV Vif, and their mutation blocked Vif-induced A3Z3 degradation. We further identified additional essential residues for FIV Vif interaction in the A3Z2 domain, allowing the generation of FIV Vif resistant A3Z2Z3. Mutated feline A3s also showed resistance to the Vif of a lion-specific FIV, indicating an evolutionary conserved Vif–A3 binding. Comparative modelling of feline A3Z2Z3 suggests that the residues interacting with FIV Vif have, unlike Vif-interacting residues in human A3s, a unique location at the domain interface of Z2 and Z3 and that the linker forms a homeobox-like domain protruding of the Z2Z3 core. HIV-2/SIV Vifs efficiently degrade feline A3Z2Z3 by possible targeting the linker stretch connecting both Z-domains. Conclusions Here we identified in feline A3s residues important for binding of FIV Vif and a unique protein domain insertion (linker). To understand Vif evolution, a structural model of the feline A3 was developed. Our results show that HIV Vif binds human A3s differently than FIV Vif feline A3s. The linker insertion is suggested to form a homeo-box domain, which is unique to A3s of cats and related species, and not found in human and mouse A3s. Together, these findings indicate a specific and different A3 evolution in cats and human. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0274-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zeli Zhang
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Qinyong Gu
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Ananda Ayyappan Jaguva Vasudevan
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Anika Hain
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Björn-Philipp Kloke
- Department of Medical Biotechnology, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225, Langen, Germany.,BioNTech RNA Pharmaceuticals GmbH, An der Goldgrube 12, 55131, Mainz, Germany
| | - Sascha Hasheminasab
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Daniel Mulnaes
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Kei Sato
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, 6068507, Japan.,CREST, Japan Science and Technology Agency, Saitama, 3220012, Japan
| | - Klaus Cichutek
- Department of Medical Biotechnology, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225, Langen, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Ignacio G Bravo
- MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center of Scientific Research (CNRS), 34394, Montpellier, France
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany.
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27
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Widderich N, Kobus S, Höppner A, Riclea R, Seubert A, Dickschat JS, Heider J, Smits SHJ, Bremer E. Biochemistry and Crystal Structure of Ectoine Synthase: A Metal-Containing Member of the Cupin Superfamily. PLoS One 2016; 11:e0151285. [PMID: 26986827 PMCID: PMC4795551 DOI: 10.1371/journal.pone.0151285] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/25/2016] [Indexed: 01/24/2023] Open
Abstract
Ectoine is a compatible solute and chemical chaperone widely used by members of the Bacteria and a few Archaea to fend-off the detrimental effects of high external osmolarity on cellular physiology and growth. Ectoine synthase (EctC) catalyzes the last step in ectoine production and mediates the ring closure of the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid through a water elimination reaction. However, the crystal structure of ectoine synthase is not known and a clear understanding of how its fold contributes to enzyme activity is thus lacking. Using the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis (Sa), we report here both a detailed biochemical characterization of the EctC enzyme and the high-resolution crystal structure of its apo-form. Structural analysis classified the (Sa)EctC protein as a member of the cupin superfamily. EctC forms a dimer with a head-to-tail arrangement, both in solution and in the crystal structure. The interface of the dimer assembly is shaped through backbone-contacts and weak hydrophobic interactions mediated by two beta-sheets within each monomer. We show for the first time that ectoine synthase harbors a catalytically important metal co-factor; metal depletion and reconstitution experiments suggest that EctC is probably an iron-dependent enzyme. We found that EctC not only effectively converts its natural substrate N-gamma-acetyl-L-2,4-diaminobutyric acid into ectoine through a cyclocondensation reaction, but that it can also use the isomer N-alpha-acetyl-L-2,4-diaminobutyric acid as its substrate, albeit with substantially reduced catalytic efficiency. Structure-guided site-directed mutagenesis experiments targeting amino acid residues that are evolutionarily highly conserved among the extended EctC protein family, including those forming the presumptive iron-binding site, were conducted to functionally analyze the properties of the resulting EctC variants. An assessment of enzyme activity and iron content of these mutants give important clues for understanding the architecture of the active site positioned within the core of the EctC cupin barrel.
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Affiliation(s)
- Nils Widderich
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Stefanie Kobus
- X-ray Facility and Crystal Farm, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Astrid Höppner
- X-ray Facility and Crystal Farm, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ramona Riclea
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute of Organic Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Andreas Seubert
- Department of Chemistry, Analytical Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute of Organic Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- * E-mail: (SS); (EB)
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany
- * E-mail: (SS); (EB)
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28
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Frieg B, Görg B, Homeyer N, Keitel V, Häussinger D, Gohlke H. Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies. PLoS Comput Biol 2016; 12:e1004693. [PMID: 26836257 PMCID: PMC4737493 DOI: 10.1371/journal.pcbi.1004693] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 12/03/2015] [Indexed: 12/15/2022] Open
Abstract
Glutamine synthetase (GS) catalyzes ATP-dependent ligation of ammonia and glutamate to glutamine. Two mutations of human GS (R324C and R341C) were connected to congenital glutamine deficiency with severe brain malformations resulting in neonatal death. Another GS mutation (R324S) was identified in a neurologically compromised patient. However, the molecular mechanisms underlying the impairment of GS activity by these mutations have remained elusive. Molecular dynamics simulations, free energy calculations, and rigidity analyses suggest that all three mutations influence the first step of GS catalytic cycle. The R324S and R324C mutations deteriorate GS catalytic activity due to loss of direct interactions with ATP. As to R324S, indirect, water-mediated interactions reduce this effect, which may explain the suggested higher GS residual activity. The R341C mutation weakens ATP binding by destabilizing the interacting residue R340 in the apo state of GS. Additionally, the mutation is predicted to result in a significant destabilization of helix H8, which should negatively affect glutamate binding. This prediction was tested in HEK293 cells overexpressing GS by dot-blot analysis: Structural stability of H8 was impaired through mutation of amino acids interacting with R341, as indicated by a loss of masking of an epitope in the glutamate binding pocket for a monoclonal anti-GS antibody by L-methionine-S-sulfoximine; in contrast, cells transfected with wild type GS showed the masking. Our analyses reveal complex molecular effects underlying impaired GS catalytic activity in three clinically relevant mutants. Our findings could stimulate the development of ATP binding-enhancing molecules by which the R324S mutant can be repaired extrinsically. Glutamine synthetase (GS) catalyzes the ATP-dependent ligation of ammonia and glutamate to glutamine, which makes the enzyme essential for human nitrogen metabolism. Three mutations in human GS, R324C, R324S, and R341C, had been identified previously that lead to a glutamine deficiency, resulting in neonatal death in the case of R324C and R341C. However, the molecular mechanisms underlying this impairment of GS activity have remained elusive. Our results from computational biophysics approaches suggest that all three mutants influence the first step of GS’ catalytic cycle, namely ATP or glutamate binding. The analyses reveal a complex set of effects including the loss of direct interactions to substrates, the involvement of water-mediated interactions that alleviate part of the mutation effect, and long-range effects between the catalytic site and structural parts distant from it. As to the latter, experimental validation is in line with our prediction of a significant destabilization of helix H8 in the R341C mutant, which should negatively affect glutamate binding. Finally, our findings could stimulate the development of ATP-binding enhancing molecules for the R324S mutant, which has been suggested to have residual activity, that way extrinsically “repairing” the mutant.
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Affiliation(s)
- Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - Boris Görg
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail: (DH); (HG)
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail: (DH); (HG)
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29
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Widderich N, Czech L, Elling FJ, Könneke M, Stöveken N, Pittelkow M, Riclea R, Dickschat JS, Heider J, Bremer E. Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus. Environ Microbiol 2016; 18:1227-48. [PMID: 26636559 DOI: 10.1111/1462-2920.13156] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/19/2015] [Accepted: 11/27/2015] [Indexed: 11/29/2022]
Abstract
Ectoine and hydroxyectoine are compatible solutes widely synthesized by members of the Bacteria to cope with high osmolarity surroundings. Inspection of 557 archaeal genomes revealed that only 12 strains affiliated with the Nitrosopumilus, Methanothrix or Methanobacterium genera harbour ectoine/hydroxyectoine gene clusters. Phylogenetic considerations suggest that these Archaea have acquired these genes through horizontal gene transfer events. Using the Thaumarchaeon 'Candidatus Nitrosopumilus maritimus' as an example, we demonstrate that the transcription of its ectABCD genes is osmotically induced and functional since it leads to the production of both ectoine and hydroxyectoine. The ectoine synthase and the ectoine hydroxylase were biochemically characterized, and their properties resemble those of their counterparts from Bacteria. Transcriptional analysis of osmotically stressed 'Ca. N. maritimus' cells demonstrated that they possess an ectoine/hydroxyectoine gene cluster (hyp-ectABCD-mscS) different from those recognized previously since it contains a gene for an MscS-type mechanosensitive channel. Complementation experiments with an Escherichia coli mutant lacking all known mechanosensitive channel proteins demonstrated that the (Nm)MscS protein is functional. Hence, 'Ca. N. maritimus' cells cope with high salinity not only through enhanced synthesis of osmostress-protective ectoines but they already prepare themselves simultaneously for an eventually occurring osmotic down-shock by enhancing the production of a safety-valve (NmMscS).
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Affiliation(s)
- Nils Widderich
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Laura Czech
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, D-28334, Bremen, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, D-28334, Bremen, Germany
| | - Nadine Stöveken
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Marco Pittelkow
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Ramona Riclea
- Kekulé-Institut for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, Gerhard-Domagk Str. 1, D-53121, Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, Gerhard-Domagk Str. 1, D-53121, Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Johann Heider
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
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30
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Jiang Y, Zhang H, Feng W, Tan T. Refined Dummy Atom Model of Mg2+ by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy. J Chem Inf Model 2015; 55:2575-86. [DOI: 10.1021/acs.jcim.5b00286] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yang Jiang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haiyang Zhang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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31
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Mollica L, Conti G, Pollegioni L, Cavalli A, Rosini E. Unveiling the Atomic-Level Determinants of Acylase–Ligand Complexes: An Experimental and Computational Study. J Chem Inf Model 2015; 55:2227-41. [DOI: 10.1021/acs.jcim.5b00535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Mollica
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Gianluca Conti
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli studi dell’Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Loredano Pollegioni
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli studi dell’Insubria, via J. H. Dunant 3, 21100 Varese, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Elena Rosini
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli studi dell’Insubria, via J. H. Dunant 3, 21100 Varese, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
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32
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Gertzen CGW, Spomer L, Smits SHJ, Häussinger D, Keitel V, Gohlke H. Mutational mapping of the transmembrane binding site of the G-protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists. Eur J Med Chem 2015; 104:57-72. [PMID: 26435512 DOI: 10.1016/j.ejmech.2015.09.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 09/06/2015] [Accepted: 09/15/2015] [Indexed: 12/31/2022]
Abstract
TGR5 (Gpbar-1, M-Bar) is a class A G-protein coupled bile acid-sensing receptor predominately expressed in brain, liver and gastrointestinal tract, and a promising drug target for the treatment of metabolic disorders. Due to the lack of a crystal structure of TGR5, the development of TGR5 agonists has been guided by ligand-based approaches so far. Three binding mode models of bile acid derivatives have been presented recently. However, they differ from one another in terms of overall orientation or with respect to the location and interactions of the cholane scaffold, or cannot explain all results from mutagenesis experiments. Here, we present an extended binding mode model based on an iterative and integrated computational and biological approach. An alignment of 68 TGR5 agonists based on this binding mode leads to a significant and good structure-based 3D QSAR model, which constitutes the most comprehensive structure-based 3D-QSAR study of TGR5 agonists undertaken so far and suggests that the binding mode model is a close representation of the "true" binding mode. The binding mode model is further substantiated in that effects predicted for eight mutations in the binding site agree with experimental analyses on the impact of these TGR5 variants on receptor activity. In the binding mode, the hydrophobic cholane scaffold of taurolithocholate orients towards the interior of the orthosteric binding site such that rings A and B are in contact with TM5 and TM6, the taurine side chain orients towards the extracellular opening of the binding site and forms a salt bridge with R79(EL1), and the 3-hydroxyl group forms hydrogen bonds with E169(5.44) and Y240(6.51). The binding mode thus differs in important aspects from the ones recently presented. These results are highly relevant for the development of novel, more potent agonists of TGR5 and should be a valuable starting point for the development of TGR5 antagonists, which could show antiproliferative effects in tumor cells.
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Affiliation(s)
- Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Lina Spomer
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute for Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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33
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Höppner A, Widderich N, Lenders M, Bremer E, Smits SHJ. Crystal structure of the ectoine hydroxylase, a snapshot of the active site. J Biol Chem 2014; 289:29570-83. [PMID: 25172507 DOI: 10.1074/jbc.m114.576769] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes that are widely synthesized by bacteria to cope physiologically with osmotic stress. They also serve as chemical chaperones and maintain the functionality of macromolecules. 5-Hydroxyectoine is produced from ectoine through a stereo-specific hydroxylation, an enzymatic reaction catalyzed by the ectoine hydroxylase (EctD). The EctD protein is a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenase superfamily and is evolutionarily well conserved. We studied the ectoine hydroxylase from the cold-adapted marine ultra-microbacterium Sphingopyxis alaskensis (Sa) and found that the purified SaEctD protein is a homodimer in solution. We determined the SaEctD crystal structure in its apo-form, complexed with the iron catalyst, and in a form that contained iron, the co-substrate 2-oxoglutarate, and the reaction product of EctD, 5-hydroxyectoine. The iron and 2-oxoglutarate ligands are bound within the EctD active site in a fashion similar to that found in other members of the dioxygenase superfamily. 5-Hydroxyectoine, however, is coordinated by EctD in manner different from that found in high affinity solute receptor proteins operating in conjunction with microbial import systems for ectoines. Our crystallographic analysis provides a detailed view into the active site of the ectoine hydroxylase and exposes an intricate network of interactions between the enzyme and its ligands that collectively ensure the hydroxylation of the ectoine substrate in a position- and stereo-specific manner.
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Affiliation(s)
- Astrid Höppner
- From the X-ray Facility and Crystal Farm, Heinrich-Heine-University at Düsseldorf, D-40225 Düsseldorf
| | - Nils Widderich
- the Department of Biology, Laboratory for Microbiology, Philipps-University at Marburg, D-35043 Marburg, the Max Planck Institute for Terrestrial Microbiology, Emeritus Group R. K. Thauer, D-35043 Marburg
| | - Michael Lenders
- the Institute of Biochemistry, Heinrich-Heine-University at Düsseldorf, D-40225 Düsseldorf, and
| | - Erhard Bremer
- the Department of Biology, Laboratory for Microbiology, Philipps-University at Marburg, D-35043 Marburg, the LOEWE-Center for Synthetic Microbiology, Philipps-University at Marburg, D-35043 Marburg, Germany
| | - Sander H J Smits
- the Institute of Biochemistry, Heinrich-Heine-University at Düsseldorf, D-40225 Düsseldorf, and
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34
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Widderich N, Höppner A, Pittelkow M, Heider J, Smits SHJ, Bremer E. Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms. PLoS One 2014; 9:e93809. [PMID: 24714029 PMCID: PMC3979721 DOI: 10.1371/journal.pone.0093809] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Ectoine and hydroxyectoine are well-recognized members of the compatible solutes and are widely employed by microorganisms as osmostress protectants. The EctABC enzymes catalyze the synthesis of ectoine from the precursor L-aspartate-β-semialdehyde. A subgroup of the ectoine producers can convert ectoine into 5-hydroxyectoine through a region-selective and stereospecific hydroxylation reaction. This compatible solute possesses stress-protective and function-preserving properties different from those of ectoine. Hydroxylation of ectoine is carried out by the EctD protein, a member of the non-heme-containing iron (II) and 2-oxoglutarate-dependent dioxygenase superfamily. We used the signature enzymes for ectoine (EctC) and hydroxyectoine (EctD) synthesis in database searches to assess the taxonomic distribution of potential ectoine and hydroxyectoine producers. Among 6428 microbial genomes inspected, 440 species are predicted to produce ectoine and of these, 272 are predicted to synthesize hydroxyectoine as well. Ectoine and hydroxyectoine genes are found almost exclusively in Bacteria. The genome context of the ect genes was explored to identify proteins that are functionally associated with the synthesis of ectoines; the specialized aspartokinase Ask_Ect and the regulatory protein EctR. This comprehensive in silico analysis was coupled with the biochemical characterization of ectoine hydroxylases from microorganisms that can colonize habitats with extremes in salinity (Halomonas elongata), pH (Alkalilimnicola ehrlichii, Acidiphilium cryptum), or temperature (Sphingopyxis alaskensis, Paenibacillus lautus) or that produce hydroxyectoine very efficiently over ectoine (Pseudomonas stutzeri). These six ectoine hydroxylases all possess similar kinetic parameters for their substrates but exhibit different temperature stabilities and differ in their tolerance to salts. We also report the crystal structure of the Virgibacillus salexigens EctD protein in its apo-form, thereby revealing that the iron-free structure exists already in a pre-set configuration to incorporate the iron catalyst. Collectively, our work defines the taxonomic distribution and salient biochemical properties of the ectoine hydroxylase protein family and contributes to the understanding of its structure.
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Affiliation(s)
- Nils Widderich
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Emeritus Group R.K. Thauer, Marburg, Germany
| | - Astrid Höppner
- X-Ray Facility and Crystal Farm, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marco Pittelkow
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- * E-mail: (SHGS); (EB)
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- * E-mail: (SHGS); (EB)
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35
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Tanne C, Golovina EA, Hoekstra FA, Meffert A, Galinski EA. Glass-forming property of hydroxyectoine is the cause of its superior function as a desiccation protectant. Front Microbiol 2014; 5:150. [PMID: 24772110 PMCID: PMC3983491 DOI: 10.3389/fmicb.2014.00150] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/21/2014] [Indexed: 11/13/2022] Open
Abstract
We were able to demonstrate that hydroxyectoine, in contrast to ectoine, is a good glass-forming compound. Fourier transform infrared and spin label electron spin resonance studies of dry ectoine and hydroxyectoine have shown that the superior glass-forming properties of hydroxyectoine result from stronger intermolecular H-bonds with the OH group of hydroxyectoine. Spin probe experiments have also shown that better molecular immobilization in dry hydroxyectoine provides better redox stability of the molecules embedded in this dry matrix. With a glass transition temperature of 87°C (vs. 47°C for ectoine) hydroxyectoine displays remarkable desiccation protection properties, on a par with sucrose and trehalose. This explains its accumulation in response to increased salinity and elevated temperature by halophiles such as Halomonas elongata and its successful application in ``anhydrobiotic engineering'' of both enzymes and whole cells.
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Affiliation(s)
- Christoph Tanne
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-University Bonn Bonn, Germany
| | - Elena A Golovina
- Laboratory of Plant Physiology, Wageningen University Wageningen, Netherlands
| | - Folkert A Hoekstra
- Laboratory of Plant Physiology, Wageningen University Wageningen, Netherlands
| | - Andrea Meffert
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-University Bonn Bonn, Germany
| | - Erwin A Galinski
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-University Bonn Bonn, Germany
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36
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Hoeppner A, Widderich N, Bremer E, Smits SHJ. Overexpression, crystallization and preliminary X-ray crystallographic analysis of the ectoine hydroxylase from Sphingopyxis alaskensis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:493-6. [PMID: 24699747 DOI: 10.1107/s2053230x14004798] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/02/2014] [Indexed: 11/10/2022]
Abstract
The ectoine hydroxylase (EctD) is a member of the non-haem-containing iron(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. Its mononuclear iron centre is a prerequisite for the activity of this enzyme and promotes the O2-dependent oxidative decarboxylation of 2-oxoglutarate, which is coupled to a two-electron oxidation of the substrate ectoine to yield 5-hydroxyectoine. An expression and purification protocol for the EctD enzyme from Sphingopyxis alaskensis was developed and the protein was crystallized using the sitting-drop vapour-diffusion method. This resulted in two different crystal forms, representing the apo and iron-bound forms of the enzyme.
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Affiliation(s)
- Astrid Hoeppner
- Crystal Farm and X-ray Facility, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Nils Widderich
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Sander H J Smits
- Institut für Biochemie, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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