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Article ; Online: Repurposing degradation pathways for modular metabolite biosynthesis in nematodes.

Wrobel, Chester J J / Schroeder, Frank C

2023 Volume 19, Issue 6, Page(s) 676–686

Abstract: Recent studies have revealed that Caenorhabditis elegans and other nematodes repurpose products from biochemical degradation pathways for the combinatorial assembly of complex modular structures that serve diverse signaling functions. Building blocks ... ...

Abstract	Recent studies have revealed that Caenorhabditis elegans and other nematodes repurpose products from biochemical degradation pathways for the combinatorial assembly of complex modular structures that serve diverse signaling functions. Building blocks from neurotransmitter, amino acid, nucleoside and fatty acid metabolism are attached to scaffolds based on the dideoxyhexose ascarylose or glucose, resulting in hundreds of modular ascarosides and glucosides. Genome-wide association studies have identified carboxylesterases as the key enzymes mediating modular assembly, enabling rapid compound discovery via untargeted metabolomics and suggesting that modular metabolite biosynthesis originates from the 'hijacking' of conserved detoxification mechanisms. Modular metabolites thus represent a distinct biosynthetic strategy for generating structural and functional diversity in nematodes, complementing the primarily polyketide synthase- and nonribosomal peptide synthetase-derived universe of microbial natural products. Although many aspects of modular metabolite biosynthesis and function remain to be elucidated, their identification demonstrates how phenotype-driven compound discovery, untargeted metabolomics and genomic approaches can synergize to facilitate the annotation of metabolic dark matter.
MeSH term(s)	Animals ; Genome-Wide Association Study ; Nematoda/metabolism ; Caenorhabditis elegans/metabolism ; Metabolomics/methods ; Nucleosides
Chemical Substances	Nucleosides
Language	English
Publishing date	2023-04-06
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/s41589-023-01301-w
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Article ; Online: Formation and function of dauer ascarosides in the nematodes Caenorhabditis briggsae and Caenorhabditis elegans.

Cohen, Sarah M / Wrobel, Chester J J / Prakash, Sharan J / Schroeder, Frank C / Sternberg, Paul W

G3 (Bethesda, Md.)

2022 Volume 12, Issue 3

Abstract: The biosynthetic pathways and functions of ascaroside signaling molecules in the nematode Caenorhabditis elegans have been studied to better understand complex, integrative developmental decision-making. Although it is known that ascarosides play ... ...

Abstract	The biosynthetic pathways and functions of ascaroside signaling molecules in the nematode Caenorhabditis elegans have been studied to better understand complex, integrative developmental decision-making. Although it is known that ascarosides play multiple roles in the development and behavior of nematode species other than C. elegans, these parallel pheromone systems have not been well-studied. Here, we show that ascarosides in the nematode Caenorhabditis briggsae are biosynthesized in the same manner as C. elegans and act to induce the alternative developmental pathway that generates the stress-resistant dauer lifestage. We show that ascr#2 is the primary component of crude dauer pheromone in C. briggsae; in contrast, C. elegans dauer pheromone relies on a combination of ascr#2, ascr#3, and several other components. We further demonstrate that Cbr-daf-22, like its C. elegans ortholog Cel-daf-22, is necessary to produce short-chain ascarosides. Moreover, Cbr-daf-22 and Cel-daf-22 mutants produce an ascaroside-independent metabolite that acts antagonistically to crude dauer pheromone and inhibits dauer formation.
MeSH term(s)	Animals ; Caenorhabditis/genetics ; Caenorhabditis/metabolism ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Larva/metabolism ; Pheromones ; Signal Transduction
Chemical Substances	Caenorhabditis elegans Proteins ; Pheromones
Language	English
Publishing date	2022-01-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac014
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Article ; Online: Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans.

Fox, Bennett W / Helf, Maximilian J / Burkhardt, Russell N / Artyukhin, Alexander B / Curtis, Brian J / Palomino, Diana Fajardo / Schroeder, Allen F / Chaturbedi, Amaresh / Tauffenberger, Arnaud / Wrobel, Chester J J / Zhang, Ying K / Lee, Siu Sylvia / Schroeder, Frank C

Nature communications

2024 Volume 15, Issue 1, Page(s) 1520

Abstract: Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression, but the ... ...

Abstract	Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, which mimics the activity of microbiota-dependent becyp#1 but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.
MeSH term(s)	Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; PPAR alpha/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Fatty Acids/metabolism ; Cyclopropanes/metabolism
Chemical Substances	Caenorhabditis elegans Proteins ; PPAR alpha ; Fatty Acids ; Cyclopropanes
Language	English
Publishing date	2024-02-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45782-2
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Article ; Online: Oligonucleotide Catabolism-Derived Gluconucleosides in

Curtis, Brian J / Schwertfeger, Tyler J / Burkhardt, Russell N / Fox, Bennett W / Andrzejewski, Jude / Wrobel, Chester J J / Yu, Jingfang / Rodrigues, Pedro R / Tauffenberger, Arnaud / Schroeder, Frank C

Journal of the American Chemical Society

2023 Volume 145, Issue 21, Page(s) 11611–11621

Abstract: Nucleosides are essential cornerstones of life, and nucleoside derivatives and synthetic analogues have important biomedical applications. Correspondingly, production of non-canonical nucleoside derivatives in animal model systems is of particular ... ...

Abstract	Nucleosides are essential cornerstones of life, and nucleoside derivatives and synthetic analogues have important biomedical applications. Correspondingly, production of non-canonical nucleoside derivatives in animal model systems is of particular interest. Here, we report the discovery of diverse glucose-based nucleosides in
MeSH term(s)	Animals ; Nucleosides ; Caenorhabditis elegans ; Oligonucleotides ; Ribonucleosides
Chemical Substances	Nucleosides ; Oligonucleotides ; Ribonucleosides
Language	English
Publishing date	2023-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c01151
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Article: Evolutionarily related host and microbial pathways regulate fat desaturation.

Fox, Bennett W / Helf, Maximilian J / Burkhardt, Russell N / Artyukhin, Alexander B / Curtis, Brian J / Palomino, Diana Fajardo / Chaturbedi, Amaresh / Tauffenberger, Arnaud / Wrobel, Chester J J / Zhang, Ying K / Lee, Siu Sylvia / Schroeder, Frank C

bioRxiv : the preprint server for biology

2023

Abstract	Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression
Language	English
Publishing date	2023-08-31
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.31.555782
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Article ; Online: Resurrecting the Bacterial Tyrosyl-tRNA Synthetase/tRNA Pair for Expanding the Genetic Code of Both E. coli and Eukaryotes.

Italia, James S / Latour, Christopher / Wrobel, Chester J J / Chatterjee, Abhishek

Cell chemical biology

2018 Volume 25, Issue 10, Page(s) 1304–1312.e5

Abstract: The bacteria-derived tyrosyl-tRNA synthetase (TyrRS)/tRNA pair was first used for unnatural amino acid (Uaa) mutagenesis in eukaryotic cells over 15 years ago. It provides an ideal platform to genetically encode numerous useful Uaas in eukaryotes. ... ...

Abstract	The bacteria-derived tyrosyl-tRNA synthetase (TyrRS)/tRNA pair was first used for unnatural amino acid (Uaa) mutagenesis in eukaryotic cells over 15 years ago. It provides an ideal platform to genetically encode numerous useful Uaas in eukaryotes. However, this pair has been engineered to charge only a small collection of Uaas to date. Development of Uaa-selective variants of this pair has been limited by technical challenges associated with a yeast-based directed evolution platform, which is currently required to alter its substrate specificity. Here we overcome this limitation by enabling its directed evolution in an engineered strain of E. coli (ATMY), where the endogenous TyrRS/tRNA pair has been functionally replaced with an archaeal counterpart. The facile E. coli-based selection system enabled rapid engineering of this pair to develop variants that selectively incorporate various Uaas, including p-boronophenylalanine, into proteins expressed in mammalian cells as well as in the ATMY strain of E. coli.
MeSH term(s)	Animals ; Archaeal Proteins/genetics ; Boron Compounds ; Directed Molecular Evolution/methods ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Genetic Code ; HEK293 Cells ; Humans ; Models, Molecular ; Phenylalanine/analogs & derivatives ; Phenylalanine/genetics ; RNA, Transfer/genetics ; Tyrosine-tRNA Ligase/genetics
Chemical Substances	Archaeal Proteins ; Boron Compounds ; Escherichia coli Proteins ; Phenylalanine (47E5O17Y3R) ; RNA, Transfer (9014-25-9) ; Tyrosine-tRNA Ligase (EC 6.1.1.1) ; 4-boronophenylalanine (UID84303EL)
Language	English
Publishing date	2018-08-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2451-9448
ISSN (online)	2451-9448
DOI	10.1016/j.chembiol.2018.07.002
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Article ; Online: A Robust Platform for Unnatural Amino Acid Mutagenesis in E. coli Using the Bacterial Tryptophanyl-tRNA synthetase/tRNA pair.

Ficaretta, Elise D / Wrobel, Chester J J / Roy, Soumya J S / Erickson, Sarah B / Italia, James S / Chatterjee, Abhishek

Journal of molecular biology

2021 Volume 434, Issue 8, Page(s) 167304

Abstract: We report the development of a robust user-friendly Escherichia coli (E. coli) expression system, derived from the BL21(DE3) strain, for site-specifically incorporating unnatural amino acids (UAAs) into proteins using engineered E. coli tryptophanyl-tRNA ...

Abstract	We report the development of a robust user-friendly Escherichia coli (E. coli) expression system, derived from the BL21(DE3) strain, for site-specifically incorporating unnatural amino acids (UAAs) into proteins using engineered E. coli tryptophanyl-tRNA synthetase (EcTrpRS)-tRNA
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Mutagenesis ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; RNA, Transfer, Trp ; Tryptophan/genetics ; Tryptophan-tRNA Ligase/genetics ; Tryptophan-tRNA Ligase/metabolism
Chemical Substances	RNA, Transfer, Trp ; Tryptophan (8DUH1N11BX) ; RNA, Transfer (9014-25-9) ; Tryptophan-tRNA Ligase (EC 6.1.1.2)
Language	English
Publishing date	2021-10-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167304
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Article: A Robust Platform for Unnatural Amino Acid Mutagenesis in E. coli Using the Bacterial Tryptophanyl-tRNA synthetase/tRNA pair

Ficaretta, Elise D. / Wrobel, Chester J.J. / Roy, Soumya J.S. / Erickson, Sarah B. / Italia, James S. / Chatterjee, Abhishek

Journal of molecular biology. 2021 Oct. 06,

2021

Abstract	We report the development of a robust user-friendly Escherichia coli (E. coli) expression system, derived from the BL21(DE3) strain, for site-specifically incorporating unnatural amino acids (UAAs) into proteins using engineered E. coli tryptophanyl-tRNA synthetase (EcTrpRS)-tRNAᵀʳᵖ pairs. This was made possible by functionally replacing the endogenous EcTrpRS-tRNAᵀʳᵖ pair in BL21(DE3) E. coli with an orthogonal counterpart from Saccharomyces cerevisiae, and reintroducing it into the resulting altered translational machinery tryptophanyl (ATMW-BL21) E. coli strain as an orthogonal nonsense suppressor. The resulting expression system benefits from the favorable characteristics of BL21(DE3) as an expression host, and is compatible with the broadly used T7-driven recombinant expression system. Furthermore, the vector expressing the nonsense-suppressing engineered EcTrpRS-tRNAᵀʳᵖ pair was systematically optimized to significantly enhance the incorporation efficiency of various tryptophan analogs. Together, the improved strain and the optimized suppressor plasmids enable efficient UAA incorporation (up to 65% of wild-type levels) into several different proteins. This robust and user-friendly platform will significantly expand the scope of the genetically encoded tryptophan-derived UAAs.
Keywords	Escherichia coli ; Saccharomyces cerevisiae ; molecular biology ; mutagenesis ; plasmids ; tryptophan ; tryptophan-tRNA ligase
Language	English
Dates of publication	2021-1006
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167304
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Article ; Online: Sex-specificity of the C. elegans metabolome.

Burkhardt, Russell N / Artyukhin, Alexander B / Aprison, Erin Z / Curtis, Brian J / Fox, Bennett W / Ludewig, Andreas H / Palomino, Diana Fajardo / Luo, Jintao / Chaturbedi, Amaresh / Panda, Oishika / Wrobel, Chester J J / Baumann, Victor / Portman, Douglas S / Lee, Siu Sylvia / Ruvinsky, Ilya / Schroeder, Frank C

Nature communications

2023 Volume 14, Issue 1, Page(s) 320

Abstract: Recent studies of animal metabolism have revealed large numbers of novel metabolites that are involved in all aspects of organismal biology, but it is unclear to what extent metabolomes differ between sexes. Here, using untargeted comparative ... ...

Abstract	Recent studies of animal metabolism have revealed large numbers of novel metabolites that are involved in all aspects of organismal biology, but it is unclear to what extent metabolomes differ between sexes. Here, using untargeted comparative metabolomics for the analysis of wildtype animals and sex determination mutants, we show that C. elegans hermaphrodites and males exhibit pervasive metabolomic differences. Several hundred small molecules are produced exclusively or in much larger amounts in one sex, including a host of previously unreported metabolites that incorporate building blocks from nucleoside, carbohydrate, lipid, and amino acid metabolism. A subset of male-enriched metabolites is specifically associated with the presence of a male germline, whereas enrichment of other compounds requires a male soma. Further, we show that one of the male germline-dependent metabolites, an unusual dipeptide incorporating N,N-dimethyltryptophan, increases food consumption, reduces lifespan, and accelerates the last stage of larval development in hermaphrodites. Our results serve as a foundation for mechanistic studies of how the genetic sex of soma and germline shape the C. elegans metabolome and provide a blueprint for the discovery of sex-dependent metabolites in other animals.
MeSH term(s)	Animals ; Male ; Caenorhabditis elegans/metabolism ; Metabolome ; Caenorhabditis elegans Proteins/metabolism ; Metabolomics/methods ; Longevity
Chemical Substances	Caenorhabditis elegans Proteins
Language	English
Publishing date	2023-01-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36040-y
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Article ; Online: Parallel pathways for serotonin biosynthesis and metabolism in C. elegans.

Yu, Jingfang / Vogt, Merly C / Fox, Bennett W / Wrobel, Chester J J / Fajardo Palomino, Diana / Curtis, Brian J / Zhang, Bingsen / Le, Henry H / Tauffenberger, Arnaud / Hobert, Oliver / Schroeder, Frank C

Nature chemical biology

2022 Volume 19, Issue 2, Page(s) 141–150

Abstract: The neurotransmitter serotonin plays a central role in animal behavior and physiology, and many of its functions are regulated via evolutionarily conserved biosynthesis and degradation pathways. Here we show that in Caenorhabditis elegans, serotonin is ... ...

Abstract	The neurotransmitter serotonin plays a central role in animal behavior and physiology, and many of its functions are regulated via evolutionarily conserved biosynthesis and degradation pathways. Here we show that in Caenorhabditis elegans, serotonin is abundantly produced in nonneuronal tissues via phenylalanine hydroxylase, in addition to canonical biosynthesis via tryptophan hydroxylase in neurons. Combining CRISPR-Cas9 genome editing, comparative metabolomics and synthesis, we demonstrate that most serotonin in C. elegans is incorporated into N-acetylserotonin-derived glucosides, which are retained in the worm body and further modified via the carboxylesterase CEST-4. Expression patterns of CEST-4 suggest that serotonin or serotonin derivatives are transported between different tissues. Last, we show that bacterial indole production interacts with serotonin metabolism via CEST-4. Our results reveal a parallel pathway for serotonin biosynthesis in nonneuronal cell types and further indicate that serotonin-derived metabolites may serve distinct signaling functions and contribute to previously described serotonin-dependent phenotypes.
MeSH term(s)	Animals ; Caenorhabditis elegans/metabolism ; Serotonin ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Tryptophan Hydroxylase/genetics ; Tryptophan Hydroxylase/metabolism ; Behavior, Animal
Chemical Substances	Serotonin (333DO1RDJY) ; Caenorhabditis elegans Proteins ; Tryptophan Hydroxylase (EC 1.14.16.4)
Language	English
Publishing date	2022-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/s41589-022-01148-7
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