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Huang R, Hua J, Ru M, Yu M, Wang L, Huang Y, Yan S, Zhang Q, Xu W. Superb Silk Hydrogels with High Adaptability, Bioactivity, and Versatility Enabled by Photo-Cross-Linking. ACS NANO 2024; 18:15312-15325. [PMID: 38809601 DOI: 10.1021/acsnano.4c05017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The exceptional biocompatibility and adaptability of hydrogels have garnered significant interest in the biomedical field for the fabrication of biomedical devices. However, conventional synthetic hydrogels still exhibit relatively weak and fragile properties. Drawing inspiration from the photosynthesis process, we developed a facile approach to achieve a harmonious combination of superior mechanical properties and efficient preparation of silk fibroin hydrogel through photo-cross-linking technology, accomplished within 60 s. The utilization of riboflavin and H2O2 enabled a sustainable cyclic photo-cross-linking reaction, facilitating the transformation from tyrosine to dityrosine and ultimately contributing to the formation of highly cross-linked hydrogels. These photo-cross-linking hydrogels exhibited excellent elasticity and restorability even after undergoing 1000 cycles of compression. Importantly, our findings presented that hydrogel-encapsulated adipose stem cells possess the ability to stimulate cell proliferation along with stem cell stemness. This was evidenced by the continuous high expression levels of OCT4 and SOX2 over 21 days. Additionally, the utilization of photo-cross-linking hydrogels can be extended to various material molding platforms, including microneedles, microcarriers, and bone screws. Consequently, this study offered a significant approach to fabricating biomedical hydrogels capable of facilitating real-time cell delivery, thereby introducing an innovative avenue for designing silk devices with exceptional machinability and adaptability in biomedical applications.
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Affiliation(s)
- Renyan Huang
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Jiahui Hua
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Min Ru
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Meng Yu
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Lu Wang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, School and Hospital of Stomatology, Shanxi Medical University, Taiyuan 030001, China
| | - Ying Huang
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Shuqin Yan
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Qiang Zhang
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Weilin Xu
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
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2
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Das D, Miller AF. A single hydrogen bond that tunes flavin redox reactivity and activates it for modification. Chem Sci 2024; 15:7610-7622. [PMID: 38784750 PMCID: PMC11110160 DOI: 10.1039/d4sc01642d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/14/2024] [Indexed: 05/25/2024] Open
Abstract
Electron bifurcation produces high-energy products based on less energetic reagents. This feat enables biological systems to exploit abundant mediocre fuel to drive vital but demanding reactions, including nitrogen fixation and CO2 capture. Thus, there is great interest in understanding principles that can be portable to man-made devices. Bifurcating electron transfer flavoproteins (Bf ETFs) employ two flavins with contrasting reactivities to acquire pairs of electrons from a modest reductant, NADH. The bifurcating flavin then dispatches the electrons individually to a high and a low reduction midpoint potential (E°) acceptor, the latter of which captures most of the energy. Maximum efficiency requires that only one electron accesses the exergonic path that will 'pay for' the production of the low-E° product. It is therefore critical that one of the flavins, the 'electron transfer' (ET) flavin, is tuned to execute single-electron (1e-) chemistry only. To learn how, and extract fundamental principles, we systematically altered interactions with the ET-flavin O2 position. Removal of a single hydrogen bond (H-bond) disfavored the formation of the flavin anionic semiquinone (ASQ) relative to the oxidized (OX) state, lowering by 150 mV and retuning the flavin's tendency for 1e-vs. 2e- reactivity. This was achieved by replacing conserved His 290 with Phe, while also replacing the supporting Tyr 279 with Ile. Although this variant binds oxidized FADs at 90% the WT level, the ASQ state of the ET-flavin is not stable in the absence of H290's H-bond, and dissociates, in contrast to the WT. Removal of this H-bond also altered the ET-flavin's covalent chemistry. While the WT ETF accumulates modified flavins whose formation is believed to rely on an anionic paraquinone methide intermediate, the FADs of the H-bond lacking variant remain unchanged over weeks. Hence the variant that destabilizes the anionic semiquinone also suppresses the anionic intermediate in flavin modification, verifying electronic similarities between these two species. These correlations suggest that the H-bond that stabilizes the crucial flavin ASQ also promotes flavin modification. The two effects may indeed be inseparable, as a Jekyll and Hydrogen bond.
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Affiliation(s)
- Debarati Das
- Department of Chemistry, University of Kentucky Lexington Kentucky USA
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3
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Liunardo JJ, Messerli S, Gregotsch A, Lang S, Schlosser K, Rückert‐Reed C, Busche T, Kalinowski J, Zischka M, Weller P, Nouioui I, Neumann‐Schaal M, Risdian C, Wink J, Mack M. Isolation, characterisation and description of the roseoflavin producer Streptomyces berlinensis sp. nov. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13266. [PMID: 38653477 PMCID: PMC11039241 DOI: 10.1111/1758-2229.13266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
The Gram-positive bacteria Streptomyces davaonensis and Streptomyces cinnabarinus have been the only organisms known to produce roseoflavin, a riboflavin (vitamin B2) derived red antibiotic. Using a selective growth medium and a phenotypic screening, we were able to isolate a novel roseoflavin producer from a German soil sample. The isolation procedure was repeated twice, that is, the same strain could be isolated from the same location in Berlin 6 months and 12 months after its first isolation. Whole genome sequencing of the novel roseoflavin producer revealed an unusual chromosomal arrangement and the deposited genome sequence of the new isolate (G + C content of 71.47%) contains 897 genes per inverted terminal repeat, 6190 genes in the core and 107 genes located on an illegitimate terminal end. We identified the roseoflavin biosynthetic genes rosA, rosB and rosC and an unusually high number of riboflavin biosynthetic genes. Overexpression of rosA, rosB and rosC in Escherichia coli and enzyme assays confirmed their predicted functions in roseoflavin biosynthesis. A full taxonomic analysis revealed that the isolate represents a previously unknown Streptomyces species and we propose the name Streptomyces berlinensis sp. nov. for this roseoflavin producer.
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Affiliation(s)
- Jimmy Jonathan Liunardo
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Sebastien Messerli
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Ann‐Kathrin Gregotsch
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Sonja Lang
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Kerstin Schlosser
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Christian Rückert‐Reed
- Medical School East Westphalia‐LippeBielefeld UniversityBielefeldGermany
- Technology Platform Genomics, Center for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Tobias Busche
- Medical School East Westphalia‐LippeBielefeld UniversityBielefeldGermany
| | - Jörn Kalinowski
- Technology Platform Genomics, Center for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Martin Zischka
- Institute for Instrumental Analytics and Bioanalytics, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Philipp Weller
- Institute for Instrumental Analytics and Bioanalytics, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Imen Nouioui
- Leibniz‐Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Meina Neumann‐Schaal
- Leibniz‐Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Chandra Risdian
- Department of Microbial Strain CollectionHelmholtz Centre for Infection ResearchBraunschweigGermany
- Research Center for Applied MicrobiologyNational Research and Innovation Agency (BRIN)BandungIndonesia
| | - Joachim Wink
- Department of Microbial Strain CollectionHelmholtz Centre for Infection ResearchBraunschweigGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐BraunschweigBraunschweigGermany
| | - Matthias Mack
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
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4
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Unusual reactivity of a flavin in a bifurcating electron-transferring flavoprotein leads to flavin modification and a charge-transfer complex. J Biol Chem 2022; 298:102606. [PMID: 36257407 PMCID: PMC9713284 DOI: 10.1016/j.jbc.2022.102606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
From the outset, canonical electron transferring flavoproteins (ETFs) earned a reputation for containing modified flavin. We now show that modification occurs in the recently recognized bifurcating (Bf) ETFs as well. In Bf ETFs, the 'electron transfer' (ET) flavin mediates single electron transfer via a stable anionic semiquinone state, akin to the FAD of canonical ETFs, whereas a second flavin mediates bifurcation (the Bf FAD). We demonstrate that the ET FAD undergoes transformation to two different modified flavins by a sequence of protein-catalyzed reactions that occurs specifically in the ET site, when the enzyme is maintained at pH 9 in an amine-based buffer. Our optical and mass spectrometric characterizations identify 8-formyl flavin early in the process and 8-amino flavins (8AFs) at later times. The latter have not previously been documented in an ETF to our knowledge. Mass spectrometry of flavin products formed in Tris or bis-tris-aminopropane solutions demonstrates that the source of the amine adduct is the buffer. Stepwise reduction of the 8AF demonstrates that it can explain a charge transfer band observed near 726 nm in Bf ETF, as a complex involving the hydroquinone state of the 8AF in the ET site with the oxidized state of unmodified flavin in the Bf site. This supports the possibility that Bf ETF can populate a conformation enabling direct electron transfer between its two flavins, as has been proposed for cofactors brought together in complexes between ETF and its partner proteins.
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5
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Barra L, Awakawa T, Abe I. Noncanonical Functions of Enzyme Cofactors as Building Blocks in Natural Product Biosynthesis. JACS AU 2022; 2:1950-1963. [PMID: 36186570 PMCID: PMC9516700 DOI: 10.1021/jacsau.2c00391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Enzymes involved in secondary metabolite biosynthetic pathways have typically evolutionarily diverged from their counterparts functioning in primary metabolism. They often catalyze diverse and complex chemical transformations and are thus a treasure trove for the discovery of unique enzyme-mediated chemistries. Besides major natural product classes, such as terpenoids, polyketides, and ribosomally or nonribosomally synthesized peptides, biosynthetic investigations of noncanonical natural product biosynthetic pathways often reveal functionally distinct enzyme chemistries. In this Perspective, we aim to highlight challenges and opportunities of biosynthetic investigations on noncanonical natural product pathways that utilize primary metabolites as building blocks, otherwise generally considered as enzyme cofactors. A focus is made on the discovered chemical and enzymological novelties.
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Affiliation(s)
- Lena Barra
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Takayoshi Awakawa
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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6
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Fortinez CM, Bloudoff K, Harrigan C, Sharon I, Strauss M, Schmeing TM. Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module. Nat Commun 2022; 13:548. [PMID: 35087027 PMCID: PMC8795117 DOI: 10.1038/s41467-022-28221-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.
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Affiliation(s)
- Camille Marie Fortinez
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Kristjan Bloudoff
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Connor Harrigan
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Itai Sharon
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Mike Strauss
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.,Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada. .,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.
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7
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A biosynthetic pathway to aromatic amines that uses glycyl-tRNA as nitrogen donor. Nat Chem 2022; 14:71-77. [PMID: 34725492 PMCID: PMC8758506 DOI: 10.1038/s41557-021-00802-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/27/2021] [Indexed: 11/12/2022]
Abstract
Aromatic amines in nature are typically installed with Glu or Gln as the nitrogen donor. Here we report a pathway that features glycyl-tRNA instead. During the biosynthesis of pyrroloiminoquinone-type natural products such as ammosamides, peptide-aminoacyl tRNA ligases append amino acids to the C-terminus of a ribosomally synthesized peptide. First, [Formula: see text] adds Trp in a Trp-tRNA-dependent reaction and the flavoprotein AmmC1 then carries out three hydroxylations of the indole ring of Trp. After oxidation to the corresponding ortho-hydroxy para-quinone, [Formula: see text] attaches Gly to the indole ring in a Gly-tRNA dependent fashion. Subsequent decarboxylation and hydrolysis results in an amino-substituted indole. Similar transformations are catalysed by orthologous enzymes from Bacillus halodurans. This pathway features three previously unknown biochemical processes using a ribosomally synthesized peptide as scaffold for non-ribosomal peptide extension and chemical modification to generate an amino acid-derived natural product.
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8
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Kar RK, Chasen S, Mroginski MA, Miller AF. Tuning the Quantum Chemical Properties of Flavins via Modification at C8. J Phys Chem B 2021; 125:12654-12669. [PMID: 34784473 DOI: 10.1021/acs.jpcb.1c07306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavins are central to countless enzymes but display different reactivities depending on their environments. This is understood to reflect modulation of the flavin electronic structure. To understand changes in orbital natures, energies, and correlation over the ring system, we begin by comparing seven flavin variants differing at C8, exploiting their different electronic spectra to validate quantum chemical calculations. Ground state calculations replicate a Hammett trend and reveal the significance of the flavin π-system. Comparison of higher-level theories establishes CC2 and ACD(2) as methods of choice for characterization of electronic transitions. Charge transfer character and electron correlation prove responsive to the identity of the substituent at C8. Indeed, bond length alternation analysis demonstrates extensive conjugation and delocalization from the C8 position throughout the ring system. Moreover, we succeed in replicating a particularly challenging UV/Vis spectrum by implementing hybrid QM/MM in explicit solvents. Our calculations reveal that the presence of nonbonding lone pairs correlates with the change in the UV/Vis spectrum observed when the 8-methyl is replaced by NH2, OH, or SH. Thus, our computations offer routes to understanding the spectra of flavins with different modifications. This is a first step toward understanding how the same is accomplished by different binding environments.
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Affiliation(s)
- Rajiv K Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Sam Chasen
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Maria-Andrea Mroginski
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Anne-Frances Miller
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.,Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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9
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Schneider C, Konjik V, Kißling L, Mack M. The novel phosphatase RosC catalyzes the last unknown step of roseoflavin biosynthesis in Streptomyces davaonensis. Mol Microbiol 2020; 114:609-625. [PMID: 32621340 DOI: 10.1111/mmi.14567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/31/2022]
Abstract
The bacterium Streptomyces davaonensis produces the antibiotic roseoflavin, which is a riboflavin (vitamin B2 ) analog. The key enzyme of roseoflavin biosynthesis is the 8-demethyl-8-amino-riboflavin-5'-phosphate (AFP) synthase RosB which synthesizes AFP from riboflavin-5'-phosphate. AFP is not a substrate for the last enzyme of roseoflavin biosynthesis the N, N-dimethyltransferase RosA, which generates roseoflavin from 8-demethyl-8-amino-riboflavin (AF). Consequently, the roseoflavin biosynthetic pathway depends on a phosphatase, which dephosphorylates AFP to AF. Here, we report on the identification and characterization of such an AFP phosphatase which we named RosC. The gene rosC is located immediately downstream of rosA and both genes are part of a cluster comprising 10 genes. Deletion of rosC from the chromosome of S. davaonensis led to reduced roseoflavin levels in the corresponding recombinant strain. In contrast to wild-type S. davaonensis, cell-free extracts of the rosC deletion strain did not catalyze dephosphorylation of AFP. RosC was purified from an overproducing Escherichia coli strain. RosC is the fastest enzyme of roseoflavin biosynthesis (kcat 31.3 ± 1.4 min-1 ). The apparent KM for the substrate AFP was 34.5 µM. Roseoflavin biosynthesis is now completely understood--it takes three enzymes (RosB, RosC, and RosA) to convert the flavin cofactor riboflavin-5'-phosphate into a potent antibiotic.
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Affiliation(s)
- Carmen Schneider
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Valentino Konjik
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Lena Kißling
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Matthias Mack
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Mannheim, Germany
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10
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Gurruchaga-Pereda J, Martínez-Martínez V, Rezabal E, Lopez X, Garino C, Mancin F, Cortajarena AL, Salassa L. Flavin Bioorthogonal Photocatalysis Toward Platinum Substrates. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02863] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Juan Gurruchaga-Pereda
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain
- CIC biomaGUNE, Paseo de Miramón 182, Donostia, 20014, Spain
| | | | - Elixabete Rezabal
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, Donostia, 20080, Spain
| | - Xabier Lopez
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, Donostia, 20080, Spain
| | - Claudio Garino
- Department of Chemistry, University of Turin, via Pietro Giuria 7, Turin, 10125, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, 35131, Italy
| | - Aitziber L. Cortajarena
- CIC biomaGUNE, Paseo de Miramón 182, Donostia, 20014, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48011, Spain
| | - Luca Salassa
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48011, Spain
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11
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Doubayashi D, Oki M, Mikami B, Uchida H. The microenvironment surrounding FAD mediates its conversion to 8-formyl-FAD in Aspergillus oryzae RIB40 formate oxidase. J Biochem 2019; 166:67-75. [PMID: 30715389 DOI: 10.1093/jb/mvz009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/29/2019] [Indexed: 11/15/2022] Open
Abstract
Aspergillus oryzae RIB40 formate oxidase has Arg87 and Arg554 near the formyl group and O(4) atom of 8-formyl-flavin adenine dinucleotide (FAD), respectively, with Asp396 neighbouring Arg554. Herein, we probed the roles of these three residues in modification of FAD to 8-formyl-FAD. Replacement of Arg87 or Arg554 with Lys or Ala decreased and abolished the modification, respectively. Replacement of Asp396 with Ala or Asn lowered the modification rate. The observation of unusual effects of maintaining pH 7.0 on the modification in R87K, R554K and D396 variants indicates initial and subsequent processes with different pH dependencies. Comparison of the initial process at pH 4.5 and 7.0 suggests that the microenvironment around Arg87 and the protonation state of Asp396 affect the initial process in the native enzyme. Comparison of the crystal structures of native and R554 variants showed that the replacements had minimal effect on catalytic site structure. The positively charged Arg87 might contribute to the formation of an anionic quinone-methide tautomer intermediate, while the positively charged Arg554, in collaboration with the negatively charged Asp396, might stabilize this intermediate and form a hydrogen bonding network with the N(5)/O(4) region, thereby facilitating efficient FAD modification.
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Affiliation(s)
- Daiju Doubayashi
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukuishi, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukuishi, Japan
| | - Bunzo Mikami
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Ujishi, Japan
| | - Hiroyuki Uchida
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukuishi, Japan
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12
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Abstract
Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similarity-based bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed.
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13
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Kapoor I, Nair SK. Structure-Guided Analyses of a Key Enzyme Involved in the Biosynthesis of an Antivitamin. Biochemistry 2018; 57:5282-5288. [PMID: 30125480 DOI: 10.1021/acs.biochem.8b00576] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RosB catalyzes the formation of 8-aminoriboflavin 5'-phosphate (AFP), the key intermediate in roseoflavin biosynthesis, from the metabolic precursors riboflavin 5'-phosphate (RP, also known as FMN) and glutamate. The conversion of the aromatic methyl group at position 8 in RP into the aromatic amine in AFP occurs via two intermediates, namely, the aldehyde 8-formyl-RP and the acid 8-carboxy-RP. To gain insights into the mechanism for this chemically challenging transformation, we utilized a structure-based approach to identify active site variants of RosB that stall the reaction at various points along the reaction coordinate. Crystal structures of individual variants in complex with different reaction intermediates, identified via mass spectroscopic analysis, illuminate conformational changes that occur at the active site during multistep conversion. These studies provide a plausible route for the progression of the reaction and a molecular rationale for the mechanism of this unusual biocatalyst.
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Augustin P, Toplak M, Fuchs K, Gerstmann EC, Prassl R, Winkler A, Macheroux P. Oxidation of the FAD cofactor to the 8-formyl-derivative in human electron-transferring flavoprotein. J Biol Chem 2018; 293:2829-2840. [PMID: 29301933 PMCID: PMC5827430 DOI: 10.1074/jbc.ra117.000846] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/14/2017] [Indexed: 11/06/2022] Open
Abstract
The heterodimeric human (h) electron-transferring flavoprotein (ETF) transfers electrons from at least 13 different flavin dehydrogenases to the mitochondrial respiratory chain through a non-covalently bound FAD cofactor. Here, we describe the discovery of an irreversible and pH-dependent oxidation of the 8α-methyl group to 8-formyl-FAD (8f-FAD), which represents a unique chemical modification of a flavin cofactor in the human flavoproteome. Furthermore, a set of hETF variants revealed that several conserved amino acid residues in the FAD-binding pocket of electron-transferring flavoproteins are required for the conversion to the formyl group. Two of the variants generated in our study, namely αR249C and αT266M, cause glutaric aciduria type II, a severe inherited disease. Both of the variants showed impaired formation of 8f-FAD shedding new light on the potential molecular cause of disease development. Interestingly, the conversion of FAD to 8f-FAD yields a very stable flavin semiquinone that exhibited slightly lower rates of electron transfer in an artificial assay system than hETF containing FAD. In contrast, the formation of 8f-FAD enhanced the affinity to human dimethylglycine dehydrogenase 5-fold, indicating that formation of 8f-FAD modulates the interaction of hETF with client enzymes in the mitochondrial matrix. Thus, we hypothesize that the FAD cofactor bound to hETF is subject to oxidation in the alkaline (pH 8) environment of the mitochondrial matrix, which may modulate electron transport between client dehydrogenases and the respiratory chain. This discovery challenges the current concepts of electron transfer processes in mitochondria.
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Affiliation(s)
- Peter Augustin
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II
| | - Marina Toplak
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II
| | - Katharina Fuchs
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II
| | | | - Ruth Prassl
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstrasse 6/IV, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II.
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Landwehr W, Kämpfer P, Glaeser SP, Rückert C, Kalinowski J, Blom J, Goesmann A, Mack M, Schumann P, Atasayar E, Hahnke RL, Rohde M, Martin K, Stadler M, Wink J. Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov. Int J Syst Evol Microbiol 2018; 68:382-393. [DOI: 10.1099/ijsem.0.002519] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wiebke Landwehr
- Department of Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Peter Kämpfer
- University of Gießen, Heinrich-Buff-Ring 26, 35392 Gießen, Germany
| | | | - Christian Rückert
- University of Bielefeld, Centere for Biotechnology, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- University of Bielefeld, Centere for Biotechnology, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jochen Blom
- University of Gießen, Heinrich-Buff-Ring 26, 35392 Gießen, Germany
| | | | - Matthias Mack
- Biotechnology Department, Institute for Technical Microbiology, Hochschule Mannheim, Paul-Wittsack-Str.10, 68163 Mannheim, Germany
| | - Peter Schumann
- Leibnitz Institute, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Ewelina Atasayar
- Leibnitz Institute, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Richard L. Hahnke
- Leibnitz Institute, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Karin Martin
- Hans Knöll Institut für Wirkstoffforschung, 07743 Jena, Germany
| | - Marc Stadler
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Joachim Wink
- Department of Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
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16
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Konjik V, Brünle S, Demmer U, Vanselow A, Sandhoff R, Ermler U, Mack M. Die Kristallstruktur von RosB: Einblicke in den Reaktionsmechanismus des ersten Mitglieds einer flavodoxinähnlichen Enzymfamilie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Valentino Konjik
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Steffen Brünle
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Amanda Vanselow
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Roger Sandhoff
- Deutsches Krebsforschungszentrum (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Deutschland
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Matthias Mack
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
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Konjik V, Brünle S, Demmer U, Vanselow A, Sandhoff R, Ermler U, Mack M. The Crystal Structure of RosB: Insights into the Reaction Mechanism of the First Member of a Family of Flavodoxin-like Enzymes. Angew Chem Int Ed Engl 2016; 56:1146-1151. [DOI: 10.1002/anie.201610292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Valentino Konjik
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Steffen Brünle
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Ulrike Demmer
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Amanda Vanselow
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Roger Sandhoff
- German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Ulrich Ermler
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Matthias Mack
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
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Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as chrysamide A from a deep-sea fungus Penicillium chrysogenum.
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