1
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Schwarz MGA, Correa PR, Almeida PSL, Mendonça-Lima L. Mycobacterium bovis BCG dodecin gene codes a functional protein despite of a start codon mutation. Tuberculosis (Edinb) 2023; 143:102400. [PMID: 37672955 DOI: 10.1016/j.tube.2023.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Dodecin is a dodecamer involved in flavin homeostasis, with interesting temperature and osmolarity endurance features in Mycobacterium tuberculosis. A single nucleotide polymorphism in the gene's start codon in BCG, converting ATG to ACG, is predicted to generate a N-terminal shorter isoform, lacking the first 7 amino acids. We previously reported that the shortened recombinant protein has reduced extremophilic features. Here we investigate if within the mycobacterial context dodecin can be produced from both alleles, carrying ATG and ACG start codons. Reporter gene assays using mcherry cloned downstream and in phase to both M.tb and BCG "upstream" regions confirms production of functional proteins. Complementation with both dod alleles similarly enhances M. smegmatis growth after entry into logarithmic phase and exposure to hydrogen peroxide, possibly implicating this protein in oxidative stress response mechanisms. Altogether these data indicate that BCG dodecin is indeed produced, notwithstanding in lower levels compared to M.tb, conferring similar phenotypes, even with the SNP altering the M.tb ATG start codon to the BCG ACG. This protein might be an interesting drug target for the development of new therapeutics against tuberculosis.
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Affiliation(s)
| | - Paloma Rezende Correa
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Paula Silva Lacerda Almeida
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Leila Mendonça-Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
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2
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Golczak A, Prukała D, Sikorska E, Gierszewski M, Cherkas V, Kwiatek D, Kubiak A, Varma N, Pędziński T, Murphree S, Cibulka R, Mrówczyńska L, Kolanowski JL, Sikorski M. Tetramethylalloxazines as efficient singlet oxygen photosensitizers and potential redox-sensitive agents. Sci Rep 2023; 13:13426. [PMID: 37591918 PMCID: PMC10435492 DOI: 10.1038/s41598-023-40536-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023] Open
Abstract
Tetramethylalloxazines (TMeAll) have been found to have a high quantum yield of singlet oxygen generation when used as photosensitizers. Their electronic structure and transition energies (S0 → Si, S0 → Ti, T1 → Ti) were calculated using DFT and TD-DFT methods and compared to experimental absorption spectra. Generally, TMeAll display an energy diagram similar to other derivatives belonging to the alloxazine class of compounds, namely π,π* transitions are accompanied by closely located n,π* transitions. Photophysical data such as quantum yields of fluorescence, fluorescence lifetimes, and nonradiative rate constants were also studied in methanol (MeOH), acetonitrile (ACN), and 1,2-dichloroethane (DCE). The transient absorption spectra were also analyzed. To assess cytotoxicity of new compounds, a hemolytic assay was performed using human red blood cells (RBC) in vitro. Subsequently, fluorescence lifetime imaging experiments (FLIM) were performed on RBC under physiological and oxidative stress conditions alone or in the presence of TMeAll allowing for pinpointing changes caused by those compounds on the intracellular environment of these cells.
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Affiliation(s)
- Anna Golczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Dorota Prukała
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Ewa Sikorska
- Poznań University of Economics and Business, Al. Niepodległości 10, 61-875, Poznan, Poland
| | - Mateusz Gierszewski
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614, Poznan, Poland
| | - Volodymyr Cherkas
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Dorota Kwiatek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Adam Kubiak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Naisargi Varma
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Tomasz Pędziński
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Shaun Murphree
- Department of Chemistry, Allegheny College, 520 N. Main Street, Meadville, PA, USA
| | - Radek Cibulka
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628, Prague 6, Czech Republic.
| | - Lucyna Mrówczyńska
- Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland.
| | - Jacek Lukasz Kolanowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Marek Sikorski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland.
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3
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Genomic analysis of heavy metal-resistant Halobacterium salinarum isolated from Sfax solar saltern sediments. Extremophiles 2022; 26:25. [PMID: 35842547 PMCID: PMC9288257 DOI: 10.1007/s00792-022-01273-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/30/2022] [Indexed: 02/06/2023]
Abstract
The draft genome sequences of five archaeal strains, isolated from Sfax solar saltern sediments and affiliated with Halobacterium salinarum, were analyzed in order to reveal their adaptive strategies to live in hypersaline environments polluted with heavy metals. The genomes of the strains (named AS1, AS2, AS8, AS11, and AS19) are found to contain 2,060,688; 2,467,461; 2,236,624; 2,432,692; and 2,428,727 bp respectively, with a G + C content of 65.5, 66.0, 67.0, and 66.2%. The majority of these genes (43.69–55.65%) are annotated as hypothetical proteins. Growth under osmotic stress is possible by genes coding for potassium uptake, sodium efflux, and kinases, as well as stress proteins, DNA repair systems, and proteasomal components. These strains harbor many genes responsible for metal transport/resistance, such as: copper-translocating P-type ATPases, ABC transporter, and cobalt-zinc-cadmium resistance protein. In addition, detoxification enzymes and secondary metabolites are also identified. The results show strain AS1, as compared to the other strains, is more adapted to heavy metals and may be used in the bioremediation of multi-metal contaminated environments. This study highlights the presence of several commercially valuable bioproducts (carotenoids, retinal proteins, exopolysaccharide, stress proteins, squalene, and siderophores) and enzymes (protease, sulfatase, phosphatase, phosphoesterase, and chitinase) that can be used in many industrial applications.
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4
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Weidenbach K, Gutt M, Cassidy L, Chibani C, Schmitz RA. Small Proteins in Archaea, a Mainly Unexplored World. J Bacteriol 2022; 204:e0031321. [PMID: 34543104 PMCID: PMC8765429 DOI: 10.1128/jb.00313-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.
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Affiliation(s)
- Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Cynthia Chibani
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
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5
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Schwarz MGA, Luzes BGC, Correa PR, da Silva-Gonçalves AJ, Machado LDA, Guimarães ACR, Mendonça-Lima L. M. bovis BCG Moreau N-Terminal Loss Leads to a Less Stable Dodecin With Lower Flavin Binding Capacity. Front Cell Infect Microbiol 2021; 11:658888. [PMID: 33869088 PMCID: PMC8044443 DOI: 10.3389/fcimb.2021.658888] [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: 01/26/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis still remains a concerning health problem worldwide. Its etiologic agent, Mycobacterium tuberculosis, continues to be the focus of research to unravel new prophylactic and therapeutic strategies against this disease. The only vaccine in use against tuberculosis is based on the in vitro attenuated strain, M. bovis BCG. Dodecin is a dodecameric complex important for flavin homeostasis in Archea and Eubacteria, and the M. tuberculosis protein is described as thermo- and halostable. M. bovis BCG Moreau, the Brazilian vaccine strain, has a single nucleotide polymorphism in the dodecin start codon, leading to a predicted loss of seven amino acids at the protein N-terminal end. In this work we aimed to characterize the effect of this mutation in the BCG Moreau protein features. Our recombinant protein assays show that the predicted BCG homolog is less thermostable than M.tb’s but maintains its dodecamerization ability, although with a lower riboflavin-binding capacity. These data are corroborated by structural analysis after comparative modeling, showing that the predicted BCG dodecin complex has a lower interaction energy among its monomers and also a distinct electrostatic surface near the flavin binding pocket. However, western blotting assays with the native proteins were unable to detect significant differences between the BCG Moreau and M.tb orthologs, indicating that other factors may be modulating protein structure/function in the bacterial context.
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Affiliation(s)
| | | | - Paloma Rezende Correa
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | - Lucas de Almeida Machado
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | - Leila Mendonça-Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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6
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Bourdeaux F, Kopp Y, Lautenschläger J, Gößner I, Besir H, Vabulas RM, Grininger M. Dodecin as carrier protein for immunizations and bioengineering applications. Sci Rep 2020; 10:13297. [PMID: 32764653 PMCID: PMC7414021 DOI: 10.1038/s41598-020-69990-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022] Open
Abstract
In bioengineering, scaffold proteins have been increasingly used to recruit molecules to parts of a cell, or to enhance the efficacy of biosynthetic or signalling pathways. For example, scaffolds can be used to make weak or non-immunogenic small molecules immunogenic by attaching them to the scaffold, in this role called carrier. Here, we present the dodecin from Mycobacterium tuberculosis (mtDod) as a new scaffold protein. MtDod is a homododecameric complex of spherical shape, high stability and robust assembly, which allows the attachment of cargo at its surface. We show that mtDod, either directly loaded with cargo or equipped with domains for non-covalent and covalent loading of cargo, can be produced recombinantly in high quantity and quality in Escherichia coli. Fusions of mtDod with proteins of up to four times the size of mtDod, e.g. with monomeric superfolder green fluorescent protein creating a 437 kDa large dodecamer, were successfully purified, showing mtDod's ability to function as recruitment hub. Further, mtDod equipped with SYNZIP and SpyCatcher domains for post-translational recruitment of cargo was prepared of which the mtDod/SpyCatcher system proved to be particularly useful. In a case study, we finally show that mtDod-peptide fusions allow producing antibodies against human heat shock proteins and the C-terminus of heat shock cognate 70 interacting protein (CHIP).
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Affiliation(s)
- Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Yannick Kopp
- Institute of Biophysical Chemistry, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Lauer Str. 15, 60438, Frankfurt am Main, Germany
| | - Julia Lautenschläger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Ines Gößner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Hüseyin Besir
- European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- PROGEN Biotechnik GmbH, 69123, Heidelberg, Germany
| | - R Martin Vabulas
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
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7
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Duan HD, Mohamed-Raseek N, Miller AF. Spectroscopic evidence for direct flavin-flavin contact in a bifurcating electron transfer flavoprotein. J Biol Chem 2020; 295:12618-12634. [PMID: 32661195 DOI: 10.1074/jbc.ra120.013174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
A remarkable charge transfer (CT) band is described in the bifurcating electron transfer flavoprotein (Bf-ETF) from Rhodopseudomonas palustris (RpaETF). RpaETF contains two FADs that play contrasting roles in electron bifurcation. The Bf-FAD accepts electrons pairwise from NADH, directs one to a lower-reduction midpoint potential (E°) carrier, and the other to the higher-E° electron transfer FAD (ET-FAD). Previous work noted that a CT band at 726 nm formed when ET-FAD was reduced and Bf-FAD was oxidized, suggesting that both flavins participate. However, existing crystal structures place them too far apart to interact directly. We present biochemical experiments addressing this conundrum and elucidating the nature of this CT species. We observed that RpaETF missing either FAD lacked the 726 nm band. Site-directed mutagenesis near either FAD produced altered yields of the CT species, supporting involvement of both flavins. The residue substitutions did not alter the absorption maximum of the signal, ruling out contributions from residue orbitals. Instead, we propose that the residue identities modulate the population of a protein conformation that brings the ET-flavin and Bf-flavin into direct contact, explaining the 726 nm band based on a CT complex of reduced ET-FAD and oxidized Bf-FAD. This is corroborated by persistence of the 726 nm species during gentle protein denaturation and simple density functional theory calculations of flavin dimers. Although such a CT complex has been demonstrated for free flavins, this is the first observation of such, to our knowledge, in an enzyme. Thus, Bf-ETFs may optimize electron transfer efficiency by enabling direct flavin-flavin contact.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
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8
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Bourdeaux F, Ludwig P, Paithankar K, Sander B, Essen LO, Grininger M, Mack M. Comparative biochemical and structural analysis of the flavin-binding dodecins from Streptomyces davaonensis and Streptomyces coelicolor reveals striking differences with regard to multimerization. MICROBIOLOGY-SGM 2020; 165:1095-1106. [PMID: 31339487 DOI: 10.1099/mic.0.000835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dodecins are small flavin-binding proteins that are widespread amongst haloarchaeal and bacterial species. Haloarchaeal dodecins predominantly bind riboflavin, while bacterial dodecins have been reported to bind riboflavin-5'-phosphate, also called flavin mononucleotide (FMN), and the FMN derivative, flavin adenine dinucleotide (FAD). Dodecins form dodecameric complexes and represent buffer systems for cytoplasmic flavins. In this study, dodecins of the bacteria Streptomyces davaonensis (SdDod) and Streptomyces coelicolor (ScDod) were investigated. Both dodecins showed an unprecedented low affinity for riboflavin, FMN and FAD when compared to other bacterial dodecins. Significant binding of FMN and FAD occurred at relatively low temperatures and under acidic conditions. X-ray diffraction analyses of SdDod and ScDod revealed that the structures of both Streptomyces dodecins are highly similar, which explains their similar binding properties for FMN and FAD. In contrast, SdDod and ScDod showed very different properties with regard to the stability of their dodecameric complexes. Site-directed mutagenesis experiments revealed that a specific salt bridge (D10-K62) is responsible for this difference in stability.
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Affiliation(s)
- Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Petra Ludwig
- Institute for Technical Microbiology, Faculty for Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
| | - Karthik Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Bodo Sander
- Unit for Structural Biology, Department of Chemistry and Biology, Philipps University Marburg, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biology, Department of Chemistry and Biology, Philipps University Marburg, 35032 Marburg, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Faculty for Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
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9
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Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica. Sci Rep 2019; 9:12158. [PMID: 31434915 PMCID: PMC6704131 DOI: 10.1038/s41598-019-47994-9] [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: 02/22/2019] [Accepted: 07/24/2019] [Indexed: 12/22/2022] Open
Abstract
Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of these microbial populations, the type of metabolism and the biogeochemical cycles. Three ecosystems can be differentiated in glaciers: supraglacial, subglacial and englacial ecosystems. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by photoautotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautotrophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the least studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a food web and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. Microorganisms were analyzed by a polyphasic approach that combines a set of -omic techniques: 16S rRNA sequencing, culturomics and metaproteomics. This combination provides key information about diversity and functions of microbial populations, especially in rare habitats. Several whole essential proteins and enzymes related to metabolism and energy production, recombination and translation were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.
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10
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Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions. Methods Enzymol 2019; 620:315-347. [PMID: 31072492 DOI: 10.1016/bs.mie.2019.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions by enabling the observation and investigation of complex sequence-structure-function and evolutionary relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) and phylogenetic reconstructions to map the functional divergence and evolutionary history of protein superfamilies. We exemplify this approach using the nitroreductase (NTR) flavoenzyme superfamily, demonstrating that SSN investigations can provide a rapid and effective means to classify groups of proteins, expose sequence similarity relationships across the global scale of a protein superfamily, and efficiently support detailed phylogenetic analyses. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes, their evolution, and their associated physiological roles.
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11
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Ludwig P, Sévin DC, Busche T, Kalinowski J, Bourdeaux F, Grininger M, Mack M. Characterization of the small flavin-binding dodecin in the roseoflavin producer Streptomyces davawensis. MICROBIOLOGY-SGM 2019; 164:908-919. [PMID: 29856311 DOI: 10.1099/mic.0.000662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Genes encoding dodecin proteins are present in almost 20 % of archaeal and in more than 50 % of bacterial genomes. Archaeal dodecins bind riboflavin (vitamin B2), are thought to play a role in flavin homeostasis and possibly also help to protect cells from radical or oxygenic stress. Bacterial dodecins were found to bind riboflavin-5'-phosphate (also called flavin mononucleotide or FMN) and coenzyme A, but their physiological function remained unknown. In this study, we set out to investigate the relevance of dodecins for flavin metabolism and oxidative stress management in the phylogenetically related bacteria Streptomyces coelicolor and Streptomyces davawensis. Additionally, we explored the role of dodecins with regard to resistance against the antibiotic roseoflavin, a riboflavin analogue produced by S. davawensis. Our results show that the dodecin of S. davawensis predominantly binds FMN and is neither involved in roseoflavin biosynthesis nor in roseoflavin resistance. In contrast to S. davawensis, growth of S. coelicolor was not reduced in the presence of plumbagin, a compound, which induces oxidative stress. Plumbagin treatment stimulated expression of the dodecin gene in S. davawensis but not in S. coelicolor. Deletion of the dodecin gene in S. davawensis generated a recombinant strain which, in contrast to the wild-type, was fully resistant to plumbagin. Subsequent metabolome analyses revealed that the S. davawensis dodecin deletion strain exhibited a very different stress response when compared to the wild-type indicating that dodecins broadly affect cellular physiology.
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Affiliation(s)
- Petra Ludwig
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
| | - Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
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12
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Atilho RM, Perkins KR, Breaker RR. Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity. RNA (NEW YORK, N.Y.) 2019; 25:23-34. [PMID: 30287481 PMCID: PMC6298564 DOI: 10.1261/rna.067975.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/02/2018] [Indexed: 05/10/2023]
Abstract
Many bacteria use flavin mononucleotide (FMN) riboswitches to control the expression of genes responsible for the biosynthesis and transport of this enzyme cofactor or its precursor, riboflavin. Rare variants of FMN riboswitches found in strains of Clostridium difficile and some other bacteria typically control the expression of proteins annotated as transporters, including multidrug efflux pumps. These RNAs no longer recognize FMN, and differ from the original riboswitch consensus sequence at nucleotide positions normally involved in binding of the ribityl and phosphate moieties of the cofactor. Representatives of one of the two variant subtypes were found to bind the FMN precursor riboflavin and the FMN degradation products lumiflavin and lumichrome. Although the biologically relevant ligand sensed by these variant FMN riboswitches remains uncertain, our findings suggest that many strains of C. difficile might use rare riboswitches to sense flavin degradation products and activate transporters for their detoxification.
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Affiliation(s)
- Ruben M Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Kevin R Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
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13
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Harold LK, Antoney J, Ahmed FH, Hards K, Carr PD, Rapson T, Greening C, Jackson CJ, Cook GM. FAD-sequestering proteins protect mycobacteria against hypoxic and oxidative stress. J Biol Chem 2018; 294:2903-2912. [PMID: 30567740 DOI: 10.1074/jbc.ra118.006237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
The ability to persist in the absence of growth triggered by low oxygen levels is a critical process for the survival of mycobacterial species in many environmental niches. MSMEG_5243 (fsq), a gene of unknown function in Mycobacterium smegmatis, is up-regulated in response to hypoxia and regulated by DosRDosS/DosT, an oxygen- and redox-sensing two-component system that is highly conserved in mycobacteria. In this communication, we demonstrate that MSMEG_5243 is a flavin-sequestering protein and henceforth refer to it as Fsq. Using an array of biochemical and structural analyses, we show that Fsq is a member of the diverse superfamily of flavin- and deazaflavin-dependent oxidoreductases (FDORs) and is widely distributed in mycobacterial species. We created a markerless deletion mutant of fsq and demonstrate that fsq is required for cell survival during hypoxia. Using fsq deletion and overexpression, we found that fsq enhances cellular resistance to hydrogen peroxide treatment. The X-ray crystal structure of Fsq, solved to 2.7 Å, revealed a homodimeric organization with FAD bound noncovalently. The Fsq structure also uncovered no potential substrate-binding cavities, as the FAD is fully enclosed, and electrochemical studies indicated that the Fsq:FAD complex is relatively inert and does not share common properties with electron-transfer proteins. Taken together, our results suggest that Fsq reduces the formation of reactive oxygen species (ROS) by sequestering free FAD during recovery from hypoxia, thereby protecting the cofactor from undergoing autoxidation to produce ROS. This finding represents a new paradigm in mycobacterial adaptation to hypoxia.
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Affiliation(s)
- Liam K Harold
- From the Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - James Antoney
- Research School of Chemistry, The Australian National University, Canberra, Australia.,The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Canberra, Australian Capital Territory, Australia, and
| | - F Hafna Ahmed
- Research School of Chemistry, The Australian National University, Canberra, Australia.,The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Canberra, Australian Capital Territory, Australia, and
| | - Kiel Hards
- From the Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Paul D Carr
- Research School of Chemistry, The Australian National University, Canberra, Australia
| | - Trevor Rapson
- The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Canberra, Australian Capital Territory, Australia, and
| | - Chris Greening
- The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Canberra, Australian Capital Territory, Australia, and .,School of Biological Sciences, Monash University, Melbourne, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Canberra, Australia,
| | - Gregory M Cook
- From the Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand, .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
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Rudroff F. Whole-cell based synthetic enzyme cascades-light and shadow of a promising technology. Curr Opin Chem Biol 2018; 49:84-90. [PMID: 30458384 DOI: 10.1016/j.cbpa.2018.10.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023]
Abstract
Mimicking Nature by biocatalytic cascade reactions in a whole-cell environment is a revolutionary development in multistep synthesis for the production of bulk and fine chemicals. In the past decade, several proof of concept success stories demonstrated the power of those synthetic cascades and paved the road for future industrial applications. Although enzymes and their promiscuity are best suited to construct such artificial pathways, the complexity and the lack of understanding of the cellular machinery slowed down this progress significantly. In this review, recent achievements in the field of whole-cell biocatalysis are described, challenges and hidden traps that have to be overcome are depicted, and strategies are illustrated how to increase overall cascade productivity.
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Affiliation(s)
- Florian Rudroff
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 163-OC, 1060 Vienna, Austria.
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15
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Scheurer M, Herbst MF, Reinholdt P, Olsen JMH, Dreuw A, Kongsted J. Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems. J Chem Theory Comput 2018; 14:4870-4883. [DOI: 10.1021/acs.jctc.8b00576] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Michael F. Herbst
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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Bourdeaux F, Hammer CA, Vogt S, Schweighöfer F, Nöll G, Wachtveitl J, Grininger M. Flavin Storage and Sequestration by Mycobacterium tuberculosis Dodecin. ACS Infect Dis 2018; 4:1082-1092. [PMID: 29608272 DOI: 10.1021/acsinfecdis.7b00237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dodecins are small flavin binding proteins occurring in archaea and bacteria. They are remarkable for binding dimers of flavins with their functional relevant aromatic isoalloxazine rings deeply covered. Bacterial dodecins are widely spread and found in a large variety of pathogens, among them Pseudomonas aeruginosa, Streptococcus pneumonia, Ralstonia solanacearum, and Mycobacterium tuberculosis ( M. tuberculosis). In this work, we seek to understand the function of dodecins from M. tuberculosis dodecin. We describe flavin binding in thermodynamic and kinetic properties and achieve mechanistic insight in dodecin function by applying spectroscopic and electrochemical methods. Intriguingly, we reveal a significant pH dependence in the affinity and specificity of flavin binding. Our data give insight in M. tuberculosis dodecin function and advance the current understanding of dodecins as flavin storage and sequestering proteins. We suggest that the dodecin in M. tuberculosis may specifically be important for flavin homeostasis during the elaborate lifestyle of this organism, which calls for the evaluation of this protein as drug target.
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Affiliation(s)
- Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Christopher A. Hammer
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Stephan Vogt
- Nöll Junior Research Group, Organic Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Felix Schweighöfer
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Gilbert Nöll
- Nöll Junior Research Group, Organic Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
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17
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Guebel DV, Torres NV. Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response of Escherichia coli: Assessment by an Optimized Factorial Microarray Analysis. Front Microbiol 2018; 9:941. [PMID: 29875739 PMCID: PMC5974110 DOI: 10.3389/fmicb.2018.00941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Background: While in eukaryotes acetylation/deacetylation regulation exerts multiple pleiotropic effects, in Escherichia coli it seems to be more limited and less known. Hence, we aimed to progress in the characterization of this regulation by dealing with three convergent aspects: the effector enzymes involved, the master regulator CRP, and the dependence on glucose availability. Methods: The transcriptional response of E. coli BW25113 was analyzed across 14 relevant scenarios. These conditions arise when the wild type and four isogenic mutants (defective in deacetylase CobB, defective in N(ε)-lysine acetyl transferase PatZ, Q- and R-type mutants of protein CRP) are studied under three levels of glucose availability (glucose-limited chemostat and glucose-excess or glucose-exhausted in batch culture). The Q-type emulates a permanent stage of CRPacetylated, whereas the R-type emulates a permanent stage of CRPdeacetylated. The data were analyzed by an optimized factorial microarray method (Q-GDEMAR). Results: (a) By analyzing one mutant against the other, we were able to unravel the true genes that participate in the interaction between ΔcobB/ΔpatZ mutations and glucose availability; (b) Increasing stages of glucose limitation appear to be associated with the up-regulation of specific sets of target genes rather than with the loss of genes present when glucose is in excess; (c) Both CRPdeacetylated and CRPacetylated produce extensive changes in specific subsets of genes, but their number and identity depend on the glucose availability; (d) In other sub-sets of genes, the transcriptional effect of CRP seems to be independent of its acetylation or deacetylation; (e) Some specific ontology functions can be associated with each of the different sets of genes detected herein. Conclusions: CRP cannot be thought of only as an effector of catabolite repression, because it acts along all the glucose conditions tested (excess, limited, and exhausted), exerting both positive and negative effects through different sets of genes. Acetylation of CRP does not seem to be a binary form of regulation, as there is not a univocal relationship between its activation/inhibitory effect and its acetylation/deacetylation stage. All the combinatorial possibilities are observed. During the exponential growth phase, CRP also exerts a very significant transcriptional effect, mainly on flagellar assembly and chemotaxis (FDR = 7.2 × 10−44).
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Affiliation(s)
| | - Néstor V Torres
- Systems Biology and Mathematical Modelling Group, Department of Biochemistry, Microbiology, Cellular Biology and Genetics, Institute of Biomedical Technologies, Center for Biomedical Research of the Canary Islands, University of La Laguna, San Cristóbal de La Laguna, Spain
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18
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Scheurer M, Brisker-Klaiman D, Dreuw A. Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg 2+-Promoted Proton Transfer. J Phys Chem B 2017; 121:10457-10466. [PMID: 29069901 DOI: 10.1021/acs.jpcb.7b08597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced biochemical reactions are ubiquitously governed by derivatives of flavin, which is a key player in a manifold of cellular redox reactions. The photoreactivity of flavins is also one of their greatest disadvantages as the molecules are sensitive to photodegradation. To prevent this unfavorable reaction, UV-light-exposed archaea bacteria, such as Halobacterium salinarum, manage the task of protecting flavin derivatives by dodecin, a protein which stores flavins and efficiently photoprotects them. In this study, we shed light on the photoprotection mechanism, i.e., the excited state quenching mechanism by dodecin using computational methodology. Molecular dynamics (MD) simulations unraveled the hydrogen bond network in the flavin binding pocket as a starting point for proton transfer upon preceding electron transfer. Using high-level ab initio quantum chemical methods, different proton transfer channels have been investigated and an energetically feasible Mg2+-promoted channel has been identified fully explaining previous experimental observations. This is the first extensive theoretical study of archaeal dodecin, furthering the understanding of its photocycle and manipulation.
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Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - Daria Brisker-Klaiman
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
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19
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Vogt S, Wenderhold-Reeb S, Nöll G. Reversible assembly of protein-DNA nanostructures triggered by mediated electron transfer. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.02.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Sánchez CG, Su Q, Wenderhold-Reeb S, Nöll G. Nanomechanical properties of protein-DNA layers with different oligonucleotide tethers. RSC Adv 2016; 6:56467-56474. [PMID: 28066548 PMCID: PMC5171221 DOI: 10.1039/c6ra10090b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/05/2016] [Indexed: 12/23/2022] Open
Abstract
The length and flexibility of the oligonucleotide tethers strongly affect the viscoelastic properties of the resulting protein–DNA layers.
The multi-ligand binding flavoprotein dodecin is reconstituted on top of flavin-terminated oligonucleotide monolayers. A detailed quartz crystal microbalance with a dissipation monitoring (QCM-D) study showing how the length and flexibility of the oligonucleotide tethers influence the stability and the viscoelastic properties of the resulting DNA–protein layers is presented. Relatively dense protein layers can be obtained, if the length of the tethers is in the same range as the diameter of dodecin. When significantly longer tethers are used, less dense layers are formed. When rather short tethers are used, the reaching area of individual tethers is too low to capture single apododecin molecules cooperatively, and the formation of stable and dense protein layers is not possible. On top of the DNA–dodecin layers additional flavin–DNA ligands may be captured to form sandwich-type DNA–protein–DNA layers. Differences in the binding and unbinding behavior of flavin-dsDNA and flavin-ssDNA ligands are measured by QCM-D and surface plasmon fluorescence spectroscopy (SPFS). Both type of ligands show relatively low kon values, which might be explained by the structural rigidity of the binding pockets allowing a ligand to enter only when it approaches precisely in the right orientation. Apparently apododecin–flavin binding follows Fischer's classic lock-and-key binding model.
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Affiliation(s)
- Cristina Gutiérrez Sánchez
- Nöll Junior Research Group , Organic Chemistry , Chem. Biol. Dept. , Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany .
| | - Qiang Su
- Nöll Junior Research Group , Organic Chemistry , Chem. Biol. Dept. , Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany .
| | - Sabine Wenderhold-Reeb
- Nöll Junior Research Group , Organic Chemistry , Chem. Biol. Dept. , Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany .
| | - Gilbert Nöll
- Nöll Junior Research Group , Organic Chemistry , Chem. Biol. Dept. , Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany .
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21
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Gutiérrez Sánchez C, Su Q, Schönherr H, Grininger M, Nöll G. Multi-Ligand-Binding Flavoprotein Dodecin as a Key Element for Reversible Surface Modification in Nano-biotechnology. ACS NANO 2015; 9:3491-3500. [PMID: 25738566 DOI: 10.1021/nn506993s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this paper the multiple (re)programming of protein-DNA nanostructures comprising generation, deletion, and reprogramming on the same flavin-DNA-modified surface is introduced. This work is based on a systematic study of the binding affinity of the multi-ligand-binding flavoprotein dodecin on flavin-terminated DNA monolayers by surface plasmon resonance and quartz crystal microbalance with dissipation (QCM-D) measurements, surface plasmon fluorescence spectroscopy (SPFS), and dynamic AFM force spectroscopy. Depending on the flavin surface coverage, a single apododecin is captured by one or more surface-immobilized flavins. The corresponding complex binding and unbinding rate constants kon(QCM) = 7.7 × 10(3) M(-1)·s(-1) and koff(QCM) = 4.5 × 10(-3) s(-1) (Kd(QCM) = 580 nM) were determined by QCM and were found to be in agreement with values for koff determined by SPFS and force spectroscopy. Even though a single apododecin-flavin bond is relatively weak, stable dodecin monolayers were formed on flavin-DNA-modified surfaces at high flavin surface coverage due to multivalent interactions between apododecin bearing six binding pockets and the surface-bound flavin-DNA ligands. If bi- or multivalent flavin ligands are adsorbed on dodecin monolayers, stable sandwich-type surface-DNA-flavin-apododecin-flavin ligand arrays are obtained. Nevertheless, the apododecin flavin complex is easily and quantitatively disassembled by flavin reduction. Binding and release of apododecin are reversible processes, which can be carried out alternatingly several times to release one type of ligand by an external redox trigger and subsequently replace it with a different ligand. Hence the versatile concept of reprogrammable functional biointerfaces with the multi-ligand-binding flavoprotein dodecin is demonstrated.
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Affiliation(s)
| | | | | | - Martin Grininger
- ∥Goethe University Frankfurt, Riedberg Campus FMLS Building, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
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Insińska-Rak M, Sikorski M. Riboflavin interactions with oxygen-a survey from the photochemical perspective. Chemistry 2014; 20:15280-91. [PMID: 25302465 DOI: 10.1002/chem.201403895] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this short review we provide some insights to the main processes that riboflavin is involved in upon absorption of a photon. We describe riboflavin properties in its interactions with oxygen, comparing them to the properties of some other singlet oxygen sensitizers. Data are provided on riboflavin photosensitizing properties in vivo and in vitro, and its properties as an endogenous singlet oxygen sensitizer are discussed. We additionally report flavin catalytic role in organic synthesis and photochemical reactivity in solutions of riboflavin and some of its derivatives.
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Affiliation(s)
- Małgorzata Insińska-Rak
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89b, 61-614 Poznań (Poland), Fax: (+48) 61 829 1555.
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Abstract
(1)H-, (11)B-, (13)C-, (15)N-, (17)O-, (19)F-, and (31)P-NMR chemical shifts of flavocoenzymes and derivatives of it, as well as of alloxazines and isoalloxazinium salts, from NMR experiments performed under various experimental conditions (e.g., dependence of the chemical shifts on temperature, concentration, solvent polarity, and pH) are reported. Also solid-state (13)C- and (15)N-NMR experiments are described revealing the anisotropic values of corresponding chemical shifts. These data, in combination with a number of coupling constants, led to a detailed description of the electronic structure of oxidized and reduced flavins. The data also demonstrate that the structure of oxidized flavin can assume a configuration deviating from coplanarity, depending on substitutions in the isoalloxazine ring, while that of reduced flavin exhibits several configurations, from almost planar to quite bended. The complexes formed between oxidized flavin and metal ions or organic molecules revealed three coordination sites with metal ions (depending on the chemical nature of the ion), and specific interactions between the pyrimidine moiety of flavin and organic molecules, mimicking specific interactions between apoflavoproteins and their coenzymes. Most NMR studies on flavoproteins were performed using (13)C- and (15)N-substituted coenzymes, either specifically enriched in the pterin moiety of flavin or uniformly labeled flavins. The chemical shifts of free flavins are used as a guide in the interpretation of the chemical shifts observed in flavoproteins. Although the hydrogen-bonding pattern in oxidized and reduced flavoproteins varies considerably, no correlation is obvious between these patterns and the corresponding redox potentials. In all reduced flavoproteins the N(1)H group of the flavocoenzyme is deprotonated, an exception is thioredoxin reductase. Three-dimensional structures of only a few flavoproteins, mostly belonging to the family of flavodoxins, have been solved. Also the kinetics of unfolding and refolding of flavodoxins has been investigated by NMR techniques. In addition, (31)P-NMR data of all so far studied flavoproteins and some (19)F-NMR spectra are discussed.
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Affiliation(s)
- Franz Müller
- , Wylstrasse 13, CH-6052, Hergiswil, Switzerland,
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Staudt H, Hoesl MG, Dreuw A, Serdjukow S, Oesterhelt D, Budisa N, Wachtveitl J, Grininger M. Directed manipulation of a flavoprotein photocycle. Angew Chem Int Ed Engl 2013; 52:8463-6. [PMID: 23818044 DOI: 10.1002/anie.201302334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Heike Staudt
- Institut für Physikalische and Theoretische Chemie, Exzellenzcluster Makromolekulare Komplexe, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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Staudt H, Hoesl MG, Dreuw A, Serdjukow S, Oesterhelt D, Budisa N, Wachtveitl J, Grininger M. Gerichtete Manipulation des Photozyklus eines Flavoproteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Yu Y, Heidel B, Parapugna TL, Wenderhold-Reeb S, Song B, Schönherr H, Grininger M, Nöll G. Das Flavoprotein Dodecin als redoxaktive Sonde für Elektronentransfer durch DNA. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Yu Y, Heidel B, Parapugna TL, Wenderhold-Reeb S, Song B, Schönherr H, Grininger M, Nöll G. The flavoprotein dodecin as a redox probe for electron transfer through DNA. Angew Chem Int Ed Engl 2013; 52:4950-3. [PMID: 23532984 PMCID: PMC3743158 DOI: 10.1002/anie.201208987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Indexed: 11/18/2022]
Affiliation(s)
- Yaming Yu
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Björn Heidel
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Tamara Lourdes Parapugna
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Sabine Wenderhold-Reeb
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Bo Song
- Physikalische Chemie I, Universität Siegen, Fakultät IV, Department für Chemie und BiologieAdolf-Reichwein-Strasse 2, 57076 Siegen (Germany)
| | - Holger Schönherr
- Physikalische Chemie I, Universität Siegen, Fakultät IV, Department für Chemie und BiologieAdolf-Reichwein-Strasse 2, 57076 Siegen (Germany)
| | - Martin Grininger
- Institut für Organische Chemie und Chemische Biologie, Buchmann Institut für Molekulare Lebenswissenschaften, Cluster of Excellence “Macromolecular Complexes”, Goethe Universität FrankfurtMax-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany)
| | - Gilbert Nöll
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
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Metabolite damage and its repair or pre-emption. Nat Chem Biol 2013; 9:72-80. [PMID: 23334546 DOI: 10.1038/nchembio.1141] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 11/13/2012] [Indexed: 01/25/2023]
Abstract
It is increasingly evident that metabolites suffer various kinds of damage, that such damage happens in all organisms and that cells have dedicated systems for damage repair and containment. First, chemical biology is demonstrating that diverse metabolites are damaged by side reactions of 'promiscuous' enzymes or by spontaneous chemical reactions, that the products are useless or toxic and that the unchecked buildup of these products can be devastating. Second, genetic and genomic evidence from prokaryotes and eukaryotes is implicating a network of new, conserved enzymes that repair damaged metabolites or somehow pre-empt damage. Metabolite (that is, small-molecule) repair is analogous to macromolecule (DNA and protein) repair and seems from comparative genomic evidence to be equally widespread. Comparative genomics also implies that metabolite repair could be the function of many conserved protein families lacking known activities. How--and how well--cells deal with metabolite damage affects fields ranging from medical genetics to metabolic engineering.
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Knaus T, Eger E, Koop J, Stipsits S, Kinsland CL, Ealick SE, Macheroux P. Reverse structural genomics: an unusual flavin-binding site in a putative protease from Bacteroides thetaiotaomicron. J Biol Chem 2012; 287:27490-8. [PMID: 22718753 DOI: 10.1074/jbc.m112.355388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of a putative protease from Bacteroides thetaiotaomicron features an unprecedented binding site for flavin mononucleotide. The flavin isoalloxazine ring is sandwiched between two tryptophan residues in the interface of the dimeric protein. We characterized the recombinant protein with regard to its affinity for naturally occurring flavin derivatives and several chemically modified flavin analogs. Dissociation constants were determined by isothermal titration calorimetry. The protein has high affinity to naturally occurring flavin derivatives, such as riboflavin, FMN, and FAD, as well as lumichrome, a photodegradation product of flavins. Similarly, chemically modified flavin analogs showed high affinity to the protein in the nanomolar range. Replacement of the tryptophan by phenylalanine gave rise to much weaker binding, whereas in the tryptophan to alanine variant, flavin binding was abolished. We propose that the protein is an unspecific scavenger of flavin compounds and may serve as a storage protein in vivo.
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Affiliation(s)
- Tanja Knaus
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
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31
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Staudt H, Oesterhelt D, Grininger M, Wachtveitl J. Ultrafast excited-state deactivation of flavins bound to dodecin. J Biol Chem 2012; 287:17637-17644. [PMID: 22451648 DOI: 10.1074/jbc.m111.331652] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dodecins, a group of flavin-binding proteins with a dodecameric quaternary structure, are able to incorporate two flavins within each of their six identical binding pockets building an aromatic tetrade with two tryptophan residues. Dodecin from the archaeal Halobacterium salinarum is a riboflavin storage device. We demonstrate that unwanted side reactions induced by reactive riboflavin species and degradation of riboflavin are avoided by ultrafast depopulation of the reactive excited state of riboflavin. Intriguingly, in this process, the staggered riboflavin dimers do not interact in ground and photoexcited states. Rather, within the tetrade assembly, each riboflavin is kept under the control of the respective adjacent tryptophan, which suggests that the stacked arrangement is a matter of optimizing the flavin load. We further identify an electron transfer in combination with a proton transfer as a central element of the effective excited state depopulation mechanism. Structural and functional comparisons of the archaeal dodecin with bacterial homologs reveal diverging evolution. Bacterial dodecins bind the flavin FMN instead of riboflavin and exhibit a clearly different binding pocket design with inverse incorporations of flavin dimers. The different adoption of flavin changes photochemical properties, making bacterial dodecin a comparably less efficient quencher of flavins. This supports a functional role different for bacterial and archaeal dodecins.
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Affiliation(s)
- Heike Staudt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Grininger
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany.
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Macheroux P, Kappes B, Ealick SE. Flavogenomics--a genomic and structural view of flavin-dependent proteins. FEBS J 2011; 278:2625-34. [PMID: 21635694 DOI: 10.1111/j.1742-4658.2011.08202.x] [Citation(s) in RCA: 208] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Riboflavin (vitamin B(2)) serves as the precursor for FMN and FAD in almost all organisms that utilize the redox-active isoalloxazine ring system as a coenzyme in enzymatic reactions. The role of flavin, however, is not limited to redox processes, as ∼ 10% of flavin-dependent enzymes catalyze nonredox reactions. Moreover, the flavin cofactor is also widely used as a signaling and sensing molecule in biological processes such as phototropism and nitrogen fixation. Here, we present a study of 374 flavin-dependent proteins analyzed with regard to their function, structure and distribution among 22 archaeal, eubacterial, protozoan and eukaryotic genomes. More than 90% of flavin-dependent enzymes are oxidoreductases, and the remaining enzymes are classified as transferases (4.3%), lyases (2.9%), isomerases (1.4%) and ligases (0.4%). The majority of enzymes utilize FAD (75%) rather than FMN (25%), and bind the cofactor noncovalently (90%). High-resolution structures are available for about half of the flavoproteins. FAD-containing proteins predominantly bind the cofactor in a Rossmann fold (∼ 50%), whereas FMN-containing proteins preferably adopt a (βα)(8)-(TIM)-barrel-like or flavodoxin-like fold. The number of genes encoding flavin-dependent proteins varies greatly in the genomes analyzed, and covers a range from ∼ 0.1% to 3.5% of the predicted genes. It appears that some species depend heavily on flavin-dependent oxidoreductases for degradation or biosynthesis, whereas others have minimized their flavoprotein arsenal. An understanding of 'flavin-intensive' lifestyles, such as in the human pathogen Mycobacterium tuberculosis, may result in valuable new intervention strategies that target either riboflavin biosynthesis or uptake.
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Affiliation(s)
- Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Graz, Austria.
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33
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Abbas CA, Sibirny AA. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 2011; 75:321-60. [PMID: 21646432 PMCID: PMC3122625 DOI: 10.1128/mmbr.00030-10] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
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Affiliation(s)
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
- University of Rzeszow, Rzeszow 35-601, Poland
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Leverrier P, Declercq JP, Denoncin K, Vertommen D, Hiniker A, Cho SH, Collet JF. Crystal structure of the outer membrane protein RcsF, a new substrate for the periplasmic protein-disulfide isomerase DsbC. J Biol Chem 2011; 286:16734-42. [PMID: 21454485 PMCID: PMC3089515 DOI: 10.1074/jbc.m111.224865] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/07/2011] [Indexed: 11/06/2022] Open
Abstract
The bacterial Rcs phosphorelay is a stress-induced defense mechanism that controls the expression of numerous genes, including those for capsular polysaccharides, motility, and virulence factors. It is a complex multicomponent system that includes the histidine kinase (RcsC) and the response regulator (RcsB) and also auxiliary proteins such as RcsF. RcsF is an outer membrane lipoprotein that transmits signals from the cell surface to RcsC. The physiological signals that activate RcsF and how RcsF interacts with RcsC remain unknown. Here, we report the three-dimensional structure of RcsF. The fold of the protein is characterized by the presence of a central 4-stranded β sheet, which is conserved in several other proteins, including the copper-binding domain of the amyloid precursor protein. RcsF, which contains four conserved cysteine residues, presents two nonconsecutive disulfides between Cys(74) and Cys(118) and between Cys(109) and Cys(124), respectively. These two disulfides are not functionally equivalent; the Cys(109)-Cys(124) disulfide is particularly important for the assembly of an active RcsF. Moreover, we show that formation of the nonconsecutive disulfides of RcsF depends on the periplasmic disulfide isomerase DsbC. We trapped RcsF in a mixed disulfide complex with DsbC, and we show that deletion of dsbC prevents the activation of the Rcs phosphorelay by signals that function through RcsF. The three-dimensional structure of RcsF provides the structural basis to understand how this protein triggers the Rcs signaling cascade.
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Affiliation(s)
- Pauline Leverrier
- From Welbio (Walloon Excellence in Life Sciences and Biotechnology)
- de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium
- Brussels Center for Redox Biology, B-1200 Brussels, Belgium
| | - Jean-Paul Declercq
- the Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium, and
| | - Katleen Denoncin
- From Welbio (Walloon Excellence in Life Sciences and Biotechnology)
- de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium
- Brussels Center for Redox Biology, B-1200 Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Annie Hiniker
- the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Seung-Hyun Cho
- From Welbio (Walloon Excellence in Life Sciences and Biotechnology)
- de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium
- Brussels Center for Redox Biology, B-1200 Brussels, Belgium
| | - Jean-François Collet
- From Welbio (Walloon Excellence in Life Sciences and Biotechnology)
- de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium
- Brussels Center for Redox Biology, B-1200 Brussels, Belgium
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Arockiasamy A, Aggarwal A, Savva CG, Holzenburg A, Sacchettini JC. Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium-binding site. Protein Sci 2011; 20:827-33. [PMID: 21370306 PMCID: PMC3125867 DOI: 10.1002/pro.607] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 02/01/2011] [Indexed: 01/07/2023]
Abstract
In eukaryotes, calcium-binding proteins play a pivotal role in diverse cellular processes, and recent findings suggest similar roles for bacterial proteins at different stages in their life cycle. Here, we report the crystal structure of calcium dodecin, Rv0379, from Mycobacterium tuberculosis with a dodecameric oligomeric assembly and a unique calcium-binding motif. Structure and sequence analysis were used to identify orthologs of Rv0379 with different ligand-binding specificity.
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Affiliation(s)
- Arulandu Arockiasamy
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTexas 77843-2128
| | - Anup Aggarwal
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTexas 77843-2128
| | - Christos G Savva
- Microscopy and Imaging Center and Department of Biology, Texas A&M University, Biological Sciences Building West, College StationTexas 77843-2257
| | - Andreas Holzenburg
- Microscopy and Imaging Center and Department of Biology, Texas A&M University, Biological Sciences Building West, College StationTexas 77843-2257
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTexas 77843-2128
- Center for Structural Biology, Institute of Biosciences and TechnologyHouston, Texas 77030
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36
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Liu F, Xiong J, Kumar S, Yang C, Ge S, Li S, Xia N, Swaminathan K. Structural and biophysical characterization of Mycobacterium tuberculosis dodecin Rv1498A. J Struct Biol 2011; 175:31-8. [PMID: 21539921 DOI: 10.1016/j.jsb.2011.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 10/18/2022]
Abstract
Dodecins (assembly of twelve monomers) are the smallest known flavoprotein with only 65-73 amino acids and are involved in binding and storage of flavins in archaea. Here we report the crystal structure of Rv1498A, a Mycobacterium tuberculosis dodecin. This bacterial dodecin structure is similar to that of other reported dodecins. Each monomer has a 3 stranded β-sheet and an α-helix perpendicular to it. This protein has polyextreme (halophilic and thermophilic) properties. Interestingly, positively and negatively charged residues aggregate separately and do not seem to contribute to thermophilic and halophilic stability. We have examined the interactions that stabilize the Rv1498A dodecamer by preparing selected point mutants that break salt bridges and hydrophobic contacts, thereby leading to collapse of the assembly.
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Affiliation(s)
- Fengxia Liu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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37
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Vinzenz X, Grosse W, Linne U, Meissner B, Essen LO. Chemical engineering of Mycobacterium tuberculosis dodecin hybrids. Chem Commun (Camb) 2011; 47:11071-3. [DOI: 10.1039/c1cc12929e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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