51
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Lee EJ, Lee OK, Lee EY. Identification of 4-Deoxy-L-Etychro-Hexoseulose Uronic Acid Reductases in an Alginolytic Bacterium Vibrio splendidus and their Uses for L-Lactate Production in an Escherichia coli Cell-Free System. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:410-423. [PMID: 29532336 DOI: 10.1007/s10126-018-9805-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/27/2018] [Indexed: 12/17/2023]
Abstract
4-Deoxy-L-erythro-hexoseulose uronic acid (DEH) reductase is a key enzyme in alginate utilizing metabolism, but the number of characterized DEH reductase is quite limited. In this study, novel two DEH reductases, VsRed-1 and VsRed-2, were identified in marine bacterium Vibrio splendidus, and the recombinant enzymes were expressed in an Escherichia coli system and purified by Ni-NTA chromatography. The optimal pH and temperature of the recombinant VsRed-1 and VsRed-2 were pH 7.5, 30 °C, and pH 7.0, 35 °C, respectively. The specific activities of VsRed-1 (776 U/mg for NADH) and VsRed-2 (176 U/mg for NADPH) were the highest among the DEH reductases reported so far. We also demonstrated that DEH could be converted to L-lactate with a yield of 76.7 and 81.9% in E. coli cell-free system containing VsRed-1 and VsRed-2 enzymes, respectively, indicating that two DEH reductases can be employed for production of biofuels and bio-chemicals from brown macroalgae biomass.
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Affiliation(s)
- Eun Jeong Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, South Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, South Korea.
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52
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The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme. Structure 2018; 26:747-758.e4. [PMID: 29681469 DOI: 10.1016/j.str.2018.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/26/2018] [Accepted: 03/20/2018] [Indexed: 12/11/2022]
Abstract
Sulfatases play a biologically important role by cleaving sulfate groups from molecules. They can be identified on the basis of signature sequences within their primary structures, and the largest family, S1, has predictable features that contribute specifically to the recognition and catalytic removal of sulfate groups. However, despite advances in the prediction and understanding of S1 sulfatases, a major question regards the molecular determinants that drive substrate recognition beyond the targeted sulfate group. Here, through analysis of an endo-4S-ι-carrageenan sulfatase (PsS1_19A) from Pseudoalteromonas sp. PS47, particularly X-ray crystal structures in complex with intact substrates, we show that specific recognition of the substrate leaving group components, in this case carbohydrate, provides the enzyme with specificity for its substrate. On the basis of these results we propose a catalytic subsite nomenclature that we anticipate will form a general foundation for understanding and describing the molecular basis of substrate recognition by sulfatases.
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54
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Alginic Acid-Aided Dispersion of Carbon Nanotubes, Graphene, and Boron Nitride Nanomaterials for Microbial Toxicity Testing. NANOMATERIALS 2018; 8:nano8020076. [PMID: 29385723 PMCID: PMC5853708 DOI: 10.3390/nano8020076] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/19/2018] [Accepted: 01/23/2018] [Indexed: 01/22/2023]
Abstract
Robust evaluation of potential environmental and health risks of carbonaceous and boron nitride nanomaterials (NMs) is imperative. However, significant agglomeration of pristine carbonaceous and boron nitride NMs due to strong van der Waals forces renders them not suitable for direct toxicity testing in aqueous media. Here, the natural polysaccharide alginic acid (AA) was used as a nontoxic, environmentally relevant dispersant with defined composition to disperse seven types of carbonaceous and boron nitride NMs, including multiwall carbon nanotubes, graphene, boron nitride nanotubes, and hexagonal boron nitride flakes, with various physicochemical characteristics. AA’s biocompatibility was confirmed by examining AA effects on viability and growth of two model microorganisms (the protozoan Tetrahymena thermophila and the bacterium Pseudomonas aeruginosa). Using 400 mg·L−1 AA, comparably stable NM (200 mg·L−1) stock dispersions were obtained by 30-min probe ultrasonication. AA non-covalently interacted with NM surfaces and improved the dispersibility of NMs in water. The dispersion stability varied with NM morphology and size rather than chemistry. The optimized dispersion protocol established here can facilitate preparing homogeneous NM dispersions for reliable exposures during microbial toxicity testing, contributing to improved reproducibility of toxicity results.
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56
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Michailidou F, Chung C, Brown MJB, Bent AF, Naismith JH, Leavens WJ, Lynn SM, Sharma SV, Goss RJM. Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins. Angew Chem Int Ed Engl 2017; 56:12492-12497. [PMID: 28786545 PMCID: PMC5656905 DOI: 10.1002/anie.201705639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/28/2017] [Indexed: 01/27/2023]
Abstract
The uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3'-deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine-5'-aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3'-deoxy pacidamycin moiety with the synthetic anti-retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.
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Affiliation(s)
- Freideriki Michailidou
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
- GSKStevenageSG1 2NYUK
| | | | | | - Andrew F. Bent
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - James H. Naismith
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | | | | | - Sunil V. Sharma
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Rebecca J. M. Goss
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
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58
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Michailidou F, Chung C, Brown MJB, Bent AF, Naismith JH, Leavens WJ, Lynn SM, Sharma SV, Goss RJM. Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Freideriki Michailidou
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
- GSK Stevenage SG1 2NY UK
| | | | | | - Andrew F. Bent
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - James H. Naismith
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | | | | | - Sunil V. Sharma
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Rebecca J. M. Goss
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
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59
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Hehemann JH, Truong LV, Unfried F, Welsch N, Kabisch J, Heiden SE, Junker S, Becher D, Thürmer A, Daniel R, Amann R, Schweder T. Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria. Environ Microbiol 2017; 19:2320-2333. [PMID: 28276126 DOI: 10.1111/1462-2920.13726] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 01/09/2023]
Abstract
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB. PelA is a large enzyme with a polysaccharide lyase family 1 (PL1) domain and a carbohydrate esterase family 8 domain, and PelB contains a PL1 domain and two carbohydrate-binding domains of family 13. Comparative phylogenomic analyses indicate that the pathway was most likely acquired from terrestrial microbes, yet we observed multi-modular orthologues only in marine bacteria. Proteomic experiments showed that P. haloplanktis ANT/505 secretes both pectate lyases into the environment in the presence of pectin. These multi-modular enzymes may therefore represent a marine innovation that enhances physical interaction with pectins to reduce loss of substrate and enzymes by diffusion. Our results revealed that marine bacteria can catabolize pectin, and highlight enzyme fusion as a potential adaptation that may facilitate microbial consumption of polymeric substrates in aquatic environments.
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Affiliation(s)
- Jan-Hendrik Hehemann
- MARUM, Center for Marine Environmental Sciences at the University of Bremen, Leobener Strasse, Bremen, D-28359, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Le Van Truong
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Institute of Biotechnology, Vietnamese Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Frank Unfried
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany.,Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Johannes Kabisch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany.,Department of Biology, Computer-aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt, D-64287, Germany
| | - Stefan E Heiden
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Sabryna Junker
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
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60
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Nishiyama R, Inoue A, Ojima T. Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01. Mar Drugs 2017; 15:md15020037. [PMID: 28216576 PMCID: PMC5334617 DOI: 10.3390/md15020037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 01/21/2023] Open
Abstract
Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%-25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%-68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An in vitro alginate-metabolizing system constructed from recFlKin, recFlAld, and previously reported alginate lyases and DEH reductase of the strain UMI-01 could convert alginate to pyruvate and glyceraldehyde-3-phosphate with an efficiency of 38%.
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Affiliation(s)
- Ryuji Nishiyama
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
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61
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Ossa F, Schnell JR, Ortega-Roldan JL. A Review of the Human Sigma-1 Receptor Structure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 964:15-29. [PMID: 28315262 DOI: 10.1007/978-3-319-50174-1_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The Sigma-1 Receptor (S1R) is a small, ligand-regulated integral membrane protein involved in cell homeostasis and the cellular stress response. The receptor has a multitude of protein and small molecule interaction partners with therapeutic potential. Newly reported structures of the human S1R in ligand-bound states provides essential insights into small molecule binding in the context of the overall protein structure. The structure also raises many interesting questions and provides an excellent starting point for understanding the molecular tricks employed by this small membrane receptor to modulate a large number of signaling events. Here, we review insights from the structures of ligand-bound S1R in the context of previous biochemical studies and propose, from a structural viewpoint, a set of important future directions.
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Affiliation(s)
- Felipe Ossa
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jason R Schnell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - José Luis Ortega-Roldan
- School of Biosciences, University of Kent, Stacey Building, Room 215B, Canterbury, CT2 7NJ, UK
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