Publications

Members of the Metabolomics Core Facility are only included in the authors list, if they contributed intellectually to a paper. In cases where we provide only standard analytical services, we kindly ask to be mentioned in the acknowledgement.

2024
Journal Article
Schaupp, S.; Arriaza-Gallardo, F. J.; Paczia, N.; Ataka, K.; Shima, S.: Acyl and CO ligands in the [Fe]-hydrogenase cofactor scramble upon photolysis. Angewandte Chemie International Edition, e202316478 (2024)
2023
Journal Article
Nattermann, M.; Wenk, S.; Pfister, P.; He, H.; Lee, S.H.; Szymanski, W.; Guntermann, N.; Zhu, F.; Nickel, L.; Wallner, C. et al.; Zarzycki, J.; Paczia, N.; Gaißert, N.; Franciò, G.; Leitner, W.; Gonzalez, R.; Erb, T. J.: Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo. Nature Communications 14 (1), 2682 (2023)
Journal Article
Marchal, D. G.; Schulz, L.; Schuster, I.; Ivanovska, J.; Paczia, N.; Prinz, S.; Zarzycki, J.; Erb, T. J.: Machine learning-supported enzyme engineering toward improved CO2-fixation of Glycolyl-CoA carboxylase. ACS Synthetic Biology 12 (12), pp. 3521 - 3530 (2023)
Journal Article
Lee, S. H.; Chou, A.; Nattermann, M.; Zhu, F.; Clomburg, J. M.; Paczia, N.; Erb, T. J.; Gonzalez, R.: Identification of 2-Hydroxyacyl-CoA synthases with high acyloin condensation activity for orthogonal one-carbon bioconversion. ACS Catalysis 13 (18), pp. 12007 - 12020 (2023)
2022
Journal Article
Arriaza-Gallardo, F. J.; Schaupp, S.; Zheng, Y.-C.; Abdul-Halim, M. F.; Hui-Jie, P.; Kahnt, J.; Angelidou, G.; Paczia, N.; Hu, X.; Costa, K. et al.; Shima, S.: The function of two radical-SAM enzymes, HcgA and HcgG, in the biosynthesis of the [Fe]-hydrogenase cofactor. Angewandte Chemie, International Edition in English 61 (50), e202213239 (2022)
Journal Article
Shi, Y.-M.; Crames, J. J.; Czech, L.; Bozhüyük, K. A. J.; Shi, Y.-N.; Hirschmann, M.; Lamberth, S.; Claus, P.; Paczia, N.; Ruckert, C. et al.; Kalinowski, J.; Bange, G.; Bode, H. B.: Genome mining enabled by biosynthetic characterization uncovers a class of benzoxazolinate-containing natural products in diverse bacteria. Angewandte Chemie, International Edition in English 61 (51), e202206106 (2022)
Journal Article
Guo, K.; Hakobyan, A.; Glatter, T.; Paczia, N.; Liesack, W.: Methylocystis sp. strain SC2 acclimatizes to increasing NH4+ levels by a precise rebalancing of enzymes and osmolyte composition. mSystems 7 (5), e0040322 (2022)
Journal Article
Pandi, A.; Diehl, C.; Yazdizadeh Kharrazi, A.; Scholz, S. A.; Bobkova, E.; Faure, L.; Nattermann, M.; Adam, D.; Chapin, N.; Foroughijabbari, Y. et al.; Moritz, C.; Paczia, N.; Cortina, N. S.; Faulon, J. L.; Erb, T. J.: A versatile active learning workflow for optimization of genetic and metabolic networks. Nature Communications 13 (1), 3876 (2022)
Journal Article
Schaupp, S.; Arriaza Gallardo, F. J.; Pan, H. J.; Kahnt, J.; Angelidou, G.; Paczia, N.; Costa, K.; Hu, X.; Shima, S.: In vitro biosynthesis of the [Fe]-hydrogenase cofactor verifies the proposed biosynthetic precursors. Angewandte Chemie, International Edition in English 61 (22), e202200994 (2022)
2021
Journal Article
Nattermann, M.; Burgener, S.; Pfister, P.; Chou, A.; Schulz, L.; Lee, S. H.; Paczia, N.; Zarzycki, J.; Gonzalez, R.; Erb, T. J.: Engineering a highly efficient carboligase for synthetic one-carbon metabolism. ACS Catalysis 11 (9), pp. 5396 - 5404 (2021)
Journal Article
Castaneda-Losada, L.; Adam, D.; Paczia, N.; Buesen, D.; Steffler, F.; Sieber, V.; Erb, T. J.; Richter, M.; Plumere, N.: Bioelectrocatalytic cofactor regeneration coupled to CO2 fixation in a redox-active hydrogel for stereoselective C-C bond formation. Angewandte Chemie, International Edition in English 60 (38), pp. 21056 - 21061 (2021)
Journal Article
Sundaram, S.; Diehl, C.; Cortina, N. S.; Bamberger, J.; Paczia, N.; Erb, T. J.: A modular in vitro platform for the production of terpenes and polyketides from CO2. Angewandte Chemie, International Edition in English 60 (30), pp. 16420 - 16425 (2021)
Journal Article
Roell, M.-S.; Schada von Borzykowski, L.; Westhoff, P.; Plett, A.; Paczia, N.; Claus, P.; Urte, S.; Erb, T. J.; Weber, A. P. M.: A synthetic C4 shuttle via the beta-hydroxyaspartate cycle in C3 plants. Proceedings of the National Academy of Sciences of the United States of America 118 (21), e2022307118 (2021)
2020
Journal Article
Hakobyan, A.; Zhu, J.; Glatter, T.; Paczia, N.; Liesack, W.: Hydrogen utilization by Methylocystis sp. strain SC2 expands the known metabolic versatility of type IIa methanotrophs. METABOLIC ENGINEERING 61, pp. 181 - 196 (2020)
Journal Article
Cotton, C. A. R.; Bernhardsgrütter, I.; He, H.; Burgener, S.; Schulz, L.; Paczia, N.; Dronsella, B.; Erban, A.; Toman, S.; Dempfle, M. et al.; De Maria, A.; Kopka, J.; Lindner, S. N.; Erb, T. J.; Bar-Even, A.: Underground isoleucine biosynthesis pathways in E. coli. ELIFE 9, e54207 (2020)
Patent
Paczia, N.; Jung, P.; Shah, P.; Linster, C.; Dimaki, M.; Svendson, W.: Microfluidic system for yeast aging analysis. WO 2020/043786 A1 (2020)
Journal Article
Burgener, S.; Cortina, N. S.; Erb, T. J.: Oxalyl-CoA Decarboxylase Enables Nucleophilic One-Carbon Extension of Aldehydes to Chiral α-Hydroxy Acids. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 59 (14), pp. 5526 - 5530 (2020)
Journal Article
Miller, T.; Beneyton, T.; Schwander, T.; Diehl, C.; Girault, M.; McLean, R.; Chotel, T.; Claus, P.; Cortina, N. S.; Baret, J.-C. et al.; Erb, T. J.: Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts. SI 368 (6491), pp. 649 - + (2020)
2019
Journal Article
Schada v. Borzyskowsi, L.; Severi, F.; Krueger, K.; Hermann, L.; Gilardet, A.; Sippel, F.; Pommerenke, B.; Claus, P.; Cortina, N. S.; Glatter, T. et al.; Zauner, S.; Zarzycki, J.; Fuchs, B. M.; Bremer, E.; Maier, U. G.; Amann I, R.; Erb, T. J.: Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle. NATURE 575 (7783), pp. 500 - + (2019)
Journal Article
Milne-Davies, B.; Helbig, C.; Wimmi, S.; Cheng, D. W. C.; Paczia, N.; Diepold, A.: Life After Secretion-Yersinia enterocolitica Rapidly Toggles Effector Secretion and Can Resume Cell Division in Response to Changing External Conditions. FRONTIERS IN MICROBIOLOGY 10, 2128 (2019)
Journal Article
Paczia, N.; Becker-Kettern, J.; Conrotte, J.-F.; Cifuente, J. O.; Guerin, M. E.; Linster, C. L.: 3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo L-Serine Synthesis. SI 58 (4), pp. 259 - 275 (2019)
Journal Article
Schymanski, E. L.; Baker, N. C.; Williams, A. J.; Singh, R. R.; Trezzi, J.-P.; Wilmes, P.; Kolber, P. L.; Kruger, R.; Paczia, N.; Linster, C. L. et al.; Balling, R.: Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges. ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS 21 (9), pp. 1426 - 1445 (2019)
Journal Article
Van Bergen, N. J.; Guo, Y.; Rankin, J.; Paczia, N.; Becker-Kettern, J.; Kremer, L. S.; Pyle, A.; Conrotte, J.-F.; Ellaway, C.; Procopis, P. et al.; Prelog, K.; Homfray, T.; Baptista, J.; Baple, E.; Wakeling, M.; Massey, S.; Kay, D. P.; Shukla, A.; Girisha, K. M.; Lewis, L. E. S.; Santra, S.; Power, R.; Daubeney, P.; Montoya, J.; Ruiz-Pesini, E.; Kovacs-Nagy, R.; Pritsch, M.; Ahting, U.; Thorburn, D. R.; Prokisch, H.; Taylor, R. W.; Christodoulou, J.; Linster, C. L.; Ellard, S.; Hakonarson, H.: NAD(P)HX dehydratase (NAXD) deficiency: a novel neurodegenerative disorder exacerbated by febrile illnesses. BRAIN 142, pp. 50 - 58 (2019)
Journal Article
Veiga-da-Cunha, M.; Chevalier, N.; Stephenne, X.; Defour, J.-P.; Paczia, N.; Ferster, A.; Achouri, Y.; Dewulf, J. P.; Linster, C. L.; Bommer, G. T. et al.; Van Schaftingen, E.: Failure to eliminate a phosphorylated glucose analog leads to neutropenia in patients with G6PT and G6PC3 deficiency. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116 (4), pp. 1241 - 1250 (2019)
2018
Journal Article
Berhardsgrütter, I.; Vögeli, B.; Wagner, T.; Peter, D.; Cortina, N. S.; Kahnt, J.; Bange, G.; Engilberge, S.; Girard, E.; Riobe, F. et al.; Maury, O.; Shima, S.; Zarzycki, J.; Erb, T. J.: The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite. NATURE CHEMICAL BIOLOGY 14 (12), p. 1127 (2018)
Journal Article
Vögeli, B.; Rosenthal, R.; Stoffel, G.; Wagner, T.; Kiefer, P.; Cortina, N. S.; Shima, S.; Erb, T. J.: InhA, the enoyl-thioester reductase from Mycobacterium tuberculosis forms a covalent adduct during catalysis. JOURNAL OF BIOLOGICAL CHEMISTRY 293 (44), pp. 17200 - 17207 (2018)
Journal Article
Vögeli, B.; Geyer, K.; Gerlinger, P.; Benkstein, S.; Cortina, N. S.; Erb, T. J.: Combining Promiscuous Acyl-CoA Oxidase and Enoyl-CoA Carboxylase/Reductases for Atypical Polyketide Extender Unit Biosynthesis. CELL CHEMICAL BIOLOGY 25 (7), p. 833 (2018)
Journal Article
Becker-Kettern, J.; Paczia, N.; Conrotte, J.-F.; Zhu, C.; Fiehn, O.; Jung, P. P.; Steinmetz, L. M.; Linster, C. L.: NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells. FEBS JOURNAL 285 (18), pp. 3376 - 3401 (2018)
Journal Article
Berger, E.; Magliaro, C.; Paczia, N.; Monzel, A. S.; Antony, P.; Linster, C. L.; Bolognin, S.; Ahluwalia, A.; Schwamborn, J. C.: Millifluidic culture improves human midbrain organoid vitality and differentiation. LAB ON A CHIP 18 (20), pp. 3172 - 3183 (2018)
Journal Article
Jung, P. P.; Zhang, Z.; Paczia, N.; Jaeger, C.; Ignac, T.; May, P.; Linster, C. L.: Natural variation of chronological aging in the Saccharomyces cerevisiae species reveals diet-dependent mechanisms of life span control. NPJ AGING AND MECHANISMS OF DISEASE 4, 3 (2018)
2017
Journal Article
Gajewski, J.; Buelens, F.; Serdjukow, S.; Janssen, M.; Cortina, N.; Grubmueler, H.; Grininger, M.: Engineering fatty acid synthases for directed polyketide production. Nature Chemical Biology 13 (4), pp. 363 - 365 (2017)
Journal Article
Peracchi, A.; Veiga-da-Cunha, M.; Kuhara, T.; Ellens, K. W.; Paczia, N.; Stroobant, V.; Seliga, A. K.; Marlaire, S.; Jaisson, S.; Bommer, G. T. et al.; Sun, J.; Huebner, K.; Linster, C. L.; Cooper, A. J. L.; van Schaftingen, E.: Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 (16), pp. E3233 - E3242 (2017)
Journal Article
Zarzycki, J.; Sutter, M.; Cortina, N. S.; Erb, T. J.; Kerfeld, C. A.: In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment. Scientific Reports 7 (1), p. 42757 (2017)
2016
Journal Article
Peter, D.; Vögeli, B.; Cortina, N. S.; Erb, T.J.: A Chemo-Enzymatic Road Map to the Synthesis of CoA Esters. Molecules 21 (4), 517 (2016)
Journal Article
Becker-Kettern, J.; Paczia, N.; Conrotte, J.-F.; Kay, D. P.; Guignard, C.; Jung, P. P.; Linster, C. L.: Saccharomyces cerevisiae Forms d-2-Hydroxyglutarate and Couples Its Degradation to d-Lactate Formation via a Cytosolic Transhydrogenase. JOURNAL OF BIOLOGICAL CHEMISTRY 291 (12), pp. 6036 - 6058 (2016)
Journal Article
Schwander, T.; Schada v. Borzyskowsi, L.; Burgener, S.; Cortina, N. S.; Erb, T. J.: A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354 (6314), pp. 900 - 904 (2016)
2014
Journal Article
Unthan, S.; Gruenberger, A.; van Ooyen, J.; Gaetgens, J.; Heinrich, J.; Paczia, N.; Wiechert, W.; Kohlheyer, D.; Noack, S.: Beyond Growth Rate 0.6: What Drives Corynebacterium glutamicum to Higher Growth Rates in Defined Medium. BIOTECHNOLOGY AND BIOENGINEERING 111 (2), pp. 359 - 371 (2014)
2013
Patent
Paczia, N.; Schramm, C.; Noack, S.: Vorrichtung und Verfahren zur Zellseparation. 102012009088 (2013)
Patent
von Lieres, E.; Motyll, S.; Paczia, N.: Probeentnahmevorrichtung und Verfahren zur Entnahme einer Probe aus einem Bioreaktor. 102012003113 (2013)
Journal Article
Gruenberger, A.; van Ooyen, J.; Paczia, N.; Rohe, P.; Schiendzielorz, G.; Eggeling, L.; Wiechert, W.; Kohlheyer, D.; Noack, S.: Beyond growth rate 0.6: Corynebacterium glutamicum cultivated in highly diluted environments. BIOTECHNOLOGY AND BIOENGINEERING 110 (1), pp. 220 - 228 (2013)
Book Chapter
Oldiges, M.; Noack, S.; Paczia, N.: Metabolomics in Biotechnology (Microbial Metabolomics). In: Metabolomics in Practice (2013)
2012
Journal Article
Grünberger, A.; Paczia, N.; Probst, C.; Schendzielorz, G.; Eggeling, L.; Noack, S.; Wiechert, W.; Kohlheyer, D.: A disposable picolitre bioreactor for cultivation and investigation of industrially relevant bacteria on the single cell level. Lab Chip 12 (11), pp. 2060 - 8 (2012)
Journal Article
Paczia, N.; Nilgen, A.; Lehmann, T.; Gaetgens, J.; Wiechert, W.; Noack, S.: Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms. MICROBIAL CELL FACTORIES 11, 122 (2012)
Journal Article
Tillack, J.; Paczia, N.; Noh, K.; Wiechert, W.; Noack, S.: Error propagation analysis for quantitative intracellular metabolomics. Metabolites 2 (4), pp. 1012 - 30 (2012)
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