Publications

Publications

 

2022

Aryal N, Chen J, Bhattarai K, Hennrich O, Handayani I, Kramer M, Straetener J, Wommer T, Berscheid A, Peter S, Reiling N, Brötz-Oesterhelt H, Geibel C, Lämmerhofer M, Mast Y, Gross H. High plasticity of the amicetin biosynthetic pathway in Streptomyces sp. SHP 22-7 led to the discovery of streptcytosine P and cytosaminomycins F and G and facilitated the production of 12F-plicacetin. J Nat Prod. https://pubs.acs.org/doi/pdf/10.1021/acs.jnatprod.1c01051 (2022).

Gavriilidou A, Kautsar SA, Zaburannyi N, Krug D, Müller R, Medema MH, Ziemert N. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat Microbiol. https://doi.org/10.1038/s41564-022-01110-2 (2022).

Gottstein J, Zaschke-Kriesche J, Unsleber S, Voitsekhovskaia I, Kulik A, Behrmann LV, Overbeck N, Stühler K, Stegmann E, Smits SHJ. New insights into the resistance mechanism for the BceAB-type transporter SaNsrFP. Sci Rep. https://doi.org/10.1038/s41598-022-08095-2 (2022).

Kim L, Lee BG, Kim M, Kim MK, Kwon DH, Kim H, Brötz-Oesterhelt H, Roh SH, Song HK. Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis. EMBO J. doi: 10.15252/embj.2021109755 (2022).

Kohga H, Mori T, Tanaka Y, Yoshikaie K, Taniguchi K, Fujimoto K, Fritz L, Schneider T, Tsukazaki T. Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms. Structure. https://doi.org/10.1016/j.str.2022.05.008 (2022).

Kuhn Cuellar L, Friedrich A, Gabernet G, de la Garza L, Fillinger S, Seyboldt A, Koch T, Zur Oven-Krockhaus S, Wanke F, Richter S, Thaiss WM, Horger M, Malek N, Harter K, Bitzer M, Nahnsen S. A data management infrastructure for the integration of imaging and omics data in life sciences. BMC Bioinformatics. doi: 10.1186/s12859-022-04584-3 (2022).

Lammers A, Lalk M, Garbeva P. Air ambulance: antimicrobial power of bacterial volatiles. Antibiotics. https://doi.org/10.3390/antibiotics11010109 (2022).

Malik IT, Hegemann JD, Brötz-Oesterhelt H. Generation of lasso peptide-based ClpP binders. Int J Mol Sci. https://doi.org/10.3390/ijms23010465 (2022). 

Mendes  SS, Marques J, Mesterházy E, Straetener J, Arts M, Pissarro T, Reginold J, Berscheid A, Bornikoel J, Kluj RM, Mayer C, Oesterhelt F, Friães S, Royo B, Schneider T, Brötz-Oesterhelt H, Romão CC, Saraiva LM. Synergetic Antimicrobial Activity and Mechanism of Clotrimazole-Linked CO-Releasing Molecules. ACS Bio & Med Chem Au. https://doi.org/10.1021/acsbiomedchemau.2c00007 (2022).

Meringdal JW, Kilian A, Li WC, Heinemann MJB, Rausch M, Schneider T, Menche D. Modular Synthesis of Halogenated Xanthones by a Divergent Coupling Strategy. J Org Chem. https://doi.org/10.1021/acs.joc.2c01157 (2022).

Morris MA, Vallmitjana A, Grein F, Schneider T, Arts M, Jones CR, Nguyen BT, Hashemian MH, Malek M, Gratton E, Nowick JS. Visualizing the mode of action and supramolecular assembly of teixobactin analogues in Bacillus subtilis. Chem Sci. https://doi.org/10.1039/d2sc01388f (2022).

Peter M, Ruland J, Depping P, Schneberger N, Severi E, Gatterdam K, Tindall S, Durand A, Heinz V, Siebrasse JP, Koenig PA, Geyer M, Ziegler C, Kubitscheck U, Thomas, GH and G Hagelueken. 2022. Structural and mechanistic analysis of tripartite ATP-independent periplasmic (TRAP) transporters. Nat Comm 13:4471, https://doi.org/10.1038/s41467-022-31907-y

Schultz D, Cuypers F, Skorka SB, Rockstroh J, Gesell Salazar M, Krieger J, Albrecht D, Völker U, Hammerschmidt S, Lalk M, Siemens N, Methling K. Bioactive lipid screening during respiratory tract infections with bacterial and viral pathogens in mice. Metabolomics. https://doi.org/10.1007/s11306-022-01898-4 (2022).

Slavetinsky CJ, Hauser JN, Gekeler C, Slavetinsky J, Geyer A, Kraus A, Heilingbrunner D, Wagner S, Tesar M, Krismer B, Kuhn S, Ernst CM, Peschel A. Sensitizing Staphylococcus aureus to antibacterial agents by decoding and blocking the lipid flippase MprF. Elife. https://doi.org/10.7554/eLife.66376 (2022).

Yin Z, Liebhart E, Stegmann E, Brötz-Oesterhelt H, Dickschat J. An isotopic probe to follow the stereochemical course of dehydratase reactions in polyketide and fatty acid biosynthesis. Org Chem Front. https://doi.org/10.1039/D2QO00272H (2022).

Wingen LM, Braun Ch, Rausch M, Gross H, Schneider T, Menche D. Versatile synthesis of pathogen specific bacterial cell wall building blocks. RSC Adv. https://doi.org/10.1039/D2RA01915A (2022).

 

2021

Beck C, Gren T, Ortiz-López FJ, Jørgensen TS, Carretero-Molina D, Martín Serrano J, Tormo JR, Oves-Costales D, Kontou EE, Mohite OS, Mingyar E, Stegmann E, Genilloud O, Weber T. Activation and identification of a griseusin cluster in Streptomyces sp. CA-256286 by employing transcriptional regulators and multi-omics methods. Molecules. https://doi.org/10.3390/molecules26216580 (2021).

Brötz-Oesterhelt H and Vorbach A. Reprogramming of the caseinolytic protease by ADEP antibiotics: Molecular mechanism, cellular consequences, therapeutic potential.  Frontiers in Molecular Biosciences. https://doi.org/10.3389/fmolb.2021.690902 (2021).

Chevrette MG, Gavriilidou A, Mantri S, Selem-Mojica N, Ziemert N, Barona-Gomez F. The confluence of big data and evolutionary genome mining for the discovery of natural products. Nat Prod Rep. https://doi.org/10.1039/D1NP00013F (2021).

Dietrich A, Steffens U, Sass P, Bierbaum G. The hypersusceptible antibiotic screening strain Staphylococcus aureus SG511-Berlin harbors multiple mutations in regulatory genes. Int J Med Microbiol. https://doi.org/10.1016/j.ijmm.2021.151545 (2021).

Drayton M, Deisinger JP, Ludwig KC, Raheem N, Müller A, Schneider T, Straus SK. Host defense peptides: Dual antimicrobial and immunomodulatory action. Int J Mol Sci. https://doi.org/10.3390/ijms222011172 (2021).

Fan SH, Liberini E, Götz F. Staphylococcus aureus genomes harbor only MpsAB-like bicarbonate transporter but not carbonic anhydrase as dissolved inorganic carbon supply system. Microbiology Spectrum.  https://doi.org/10.1128/Spectrum.00970-21 (2021).

Fišarová L, Botka T, Du X, Mašlaňová I, Bárdy P, Pantůček R, Benešík M, Roudnický P, Winstel V, Larsen J, Rosenstein R, Peschel A, Doškař J. Staphylococcus epidermidis phages transduce antimicrobial resistance plasmids and mobilize chromosomal islands. mSphere. https://doi.org/10.1128/mSphere.00223-21  (2021).

Greinacher A, Selleng K, Palankar R, Wesche J, Handtke S, Wolff M, Aurich K, Lalk M, Methling K, Volker U, Hentschker C, Michalik S, Steil L, Reder A, Schönborn L, Beer M, Franzke K, Büttner A, Fehse B, Stavrou EX, Rangaswamy C, Mailer RK, Englert H, Frye M, Thiele T, Kochanek S, Krutzke L, Siegerist F, Endlich N, Warkentin TE, Renné T. Insights in ChAdOx1 nCov-19 Vaccine-induced immune thrombotic thrombocytopenia (VITT). Blood. https://doi.org/10.1182/blood.2021013231 (2021).
 
Guo Y, Pfahler N, Voelpel S, Stehle T. Cell wall glycosylation in Staphylococcus aureus: Targeting the Tar glycosyltransferases. Curr Opin Struct Biol. https://doi.org/10.1016/j.sbi.2021.01.003 (2021).
 
Handayani I, Saad H, Ratnakomala S, Lisdiyanti P, Kusharyoto W, Krause J, Kulik A, Wohlleben W, Aziz S, Gross H, Gavriilidou A, Ziemert N, Mast Y. Mining Indonesian microbial biodiversity for novel natural compounds by a combined genome mining and molecular networking approach. Marine Drugs. https://doi.org/10.3390/md19060316 (2021).
 
Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol. https://doi.org/10.1038/s41579-021-00569-w (2021).
 
Illigmann A, Thoma Y, Pan S, Reinhardt L, Brötz-Oesterhelt H. Contribution of the Clp protease to bacterial survival and mitochondrial homoeostasis. Microb Physiol. https://doi.org/10.1159/000517718 (2021).
 
Izoré T, Candace Ho YT, Kaczmarski JA, Gavriilidou A, Chow KH, Steer DL, Goode RJA, Schittenhelm RB, Tailhades J, Tosin M, Challis GL, Krenske EH, Ziemert N, Jackson CJ, Cryle MJ. Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity. Nature Communications. https://doi.org/10.1038/s41467-021-22623-0 (2021).
 
Kengmo Tchoupa A, Eijkelkamp BA, Peschel A. Bacterial adaptation strategies to host-derived fatty acids. Trends Microbiol. https://doi.org/10.1016/j.tim.2021.06.002 (2021).
 
Luo M, Xu H, Dong Y, Shen K, Lu J, Yin Z, Qi M, Sun G, Tang L, Xiang J, Deng Z, Dickschat JS, Sun Y. The mechanism of dehydrating bimodules in trans-acyltransferase polyketide biosynthesis: A showcase study on hepatoprotective hangtaimycin, Angew Chem Int Ed. https://doi.org/10.1002/anie.202106250 (2021).
 
Menche D. Design and synthesis of simplified polyketide analogs: New modalities beyond the rule of 5. ChemMedChem. https://doi.org/10.1002/cmdc.202100150 (2021).
 
Müller M, Calvert C, Hottmann I, Kluj RM, Teufel T, Balbuchta K, Engelbrecht A, Selim KA, Xu Q, Borisova M, Titz A, Mayer C. The exo-β-N-acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosamini-dases. J Biol Chem. https://doi.org/10.1016/j.jbc.2021.100519 (2021).
 
Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas M-E, Macek B. An integrated workflow for enhanced taxonomic and functional coverage of the mouse faecal metaproteome. Gut microbes. https://doi.org/10.1080/19490976.2021.1994836 (2021).
 
Reithuber E, Wixe T, Ludwig KC, Müller A, Uvell H, Grein F, Lindgren AEG, Muschiol S, Nannapaneni P, Eriksson A, Schneider T, Normark S, Henriques-Normark B, Almqvist F, Mellroth P. THCz: Small molecules with antimicrobial activity that block cell wall lipid intermediates. PNAS. https://doi.org/10.1073/pnas.2108244118 (2021).
 
Scheeff S, Rivière S, Ruiz J, Dedenbach S, Menche D. Modular total synthesis of iso-archazolids and archazologs. J Org Chem. https://doi.org/10.1021/acs.joc.1c00946 (2021).
 
Semanjski M, Gratani FL, Englert T, Nashier P, Beke V, Nalpas N, Germain E, George S, Wolz C, Gerdes K, Macek B. Proteome dynamics during antibiotic persistence and resuscitation. mSystems, in press. https://doi.org/10.1128/mSystems.00549-21 (2021).
 
Silber N, Mayer C, Matos de Opitz CL, Sass P. Progression of the late-stage divisome is unaffected by the depletion of the cytoplasmic FtsZ pool. Commun Biol. https://doi.org/10.1038/s42003-021-01789-9 (2021).
 
Spindler S, Wingen LM, Schönenbroicher M, Seul M, Adamek M, Essig S, Kurz M, Ziemert N, Menche D. Modular fragment synthesis and bioinformatic analysis propose a revised vancoresmycin stereoconfiguration. (Honorary graphical illustration of the cover art) Org Lett. https://doi.org/10.1021/acs.orglett.0c03957 (2021).
 
Torres Salazar BO, Heilbronner S, Peschel A, Krismer B. Secondary metabolites governing microbiome interaction of staphylococcal pathogens and commensals. Microb Physiol. https://doi.org/10.1159/000517082 (2021).
 
Walter A, Friz S, Mayer C. Chitin, chitin oligosaccharide, and chitin disaccharide metabolism of Escherichia coli Revisited: Reassignment of the roles of ChiA, ChbR, ChbF, and ChbG. Microb Physiol. https://doi.org/10.1159/000515178 (2021).
 
Wewer W, Peisker H, Gutbrod K, Al-Bahra M, Menche D, Ngongeh Amambo G, Fombad FF, Jelil Njouendou A, Pfarr K, Wanji S, Hoerauf A, Dörmann P. Urine metabolites for the identification of Onchocerca volvulus infections in patients from Cameroon. Parasites Vectors. https://doi.org/10.1186/s13071-021-04893-1 (2021).
 
Wirtz DA, Ludwig KC, Arts M, Marx CE, Krannich S, Barac P, Kehraus S, Josten M, Henrichfreise B, Müller A, König GM, Peoples AJ, Nitti A, Spoering AL, Ling LL, Lewis K, Crüsemann M, Schneider T. Biosynthesis and mechanism of action of the cell wall targeting antibiotic hypeptin. Angewandte Chemie. https://doi.org/10.1002/ange.202102224 (2021).
 
Yin Z, Dickschat JS. Cis double bond formation in polyketide biosynthesis, Nat Prod Rep. https://doi.org/10.1039/D0NP00091D (2021).
 
 

2020

Babczyk A, Wingen LM, Menche D. Optimized and scalable synthesis of carba-α-D-glucosamine. Eur. J. Org. Chem. https://doi.org/10.1002/ejoc.202001203 (2020).

Chen J, Frediansyah A, Männle D, Straetener J, Brötz-Oesterhelt H, Ziemert N, Kaysser L, Gross H. New nocobactin derivatives with antimuscarinic activity, terpenibactins A-C, revealed by genome mining of Nocardia terpenica IFM 0406. Chembiochem. https://doi.org/10.1002/cbic.202000062 (2020).

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0439-x (2020).

Grein F, Müller A, Scherer KM, Liu X, Ludwig KC, Klöckner A, Strach M, Sahl HG, Kubitscheck U, Schneider T. Ca2+- Daptomycin targets cell wall biosynthesis by forming a tripartite complex with undecaprenyl-coupled intermediates and membrane lipids. Nature Communication. https://doi.org/10.1038/s41467-020-15257-1 (2020).

Krauss S, Zipperer A, Wirtz S, Saur J, Konnerth MC, Heilbronner S, Torres Salazar BO, Grond S, Krismer B, Peschel A. Secretion of and self-resistance to the novel fibupeptide antimicrobial lugdunin by distinct ABC transporters in Staphylococcus lugdunensis. Antimicrob Agents Chemother.https://aac.asm.org/content/65/1/e01734-20 (2020). 

Kumuthini J, Chimenti M, Nahnsen S, Peltzer A, Meraba R, McFadyen R, Wells G, Taylor D, Maienschein-Cline M, Li JL, Thimmapuram J, Murthy-Karuturi R, Zass L. Ten simple rules for providing effective bioinformatics research support. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1007531 (2020).

Malik IT, Pereira R, Vielberg MT, Mayer C, Straetener J, Thomy D, Famulla K, Castro H, Sass P, Groll M, Brötz-Oesterhelt H. Functional characterisation of ClpP mutations conferring resistance to acyldepsipeptide antibiotics in Firmicutes. Chembiochem. https://doi.org/10.1002/cbic.201900787 (2020).

Matos de Opitz CL, Sass P. Tackling antimicrobial resistance by exploring new mechanisms of antibiotic action. Fut Microbiol. https://doi.org/10.2217/fmb-2020-0048 (2020).

Nega M, Tribelli PM, Hipp K, Stahl M, Götz F. New insights in the coordinated amidase and glucosaminidase activity of the major autolysin (Atl) in Staphylococcus aureus. Commun Biol. https://doi.org/10.1038/s42003-020-01405-2 (2020).

Nguyen MT, Matsuo M, Niemann S, Herrmann M, Götz F. Lipoproteins in Gram-positive bacteria: abundance, function, fitness. Front Microbiol 11:582582. https://doi.org/10.3389/fmicb.2020.582582 (2020).

Raue S, Fan S-H, Rosenstein R, Zabel S, Luqman A, Nieselt K, Götz F. The genome of Staphylococcus epidermidis O47. Front Microbiol. https://doi.org/10.3389/fmicb.2020.02061 (2020).

Rivière S, Vielmuth C, Ennenbach C, Abdelrahman a, Lemke C, Gütschow M, Müller CE, Menche D. Design, synthesis and biological evaluation of highly potent simplified archazolids. Chem Med Chem. https://doi.org/10.1002/cmdc.202000154 (2020).

Sassine J, Sousa J, Lalk M, Daniel RA, Vollmer W. Cell morphology maintenance in Bacillus subtilis through balanced peptidoglycan synthesis and hydrolysis. Sci Rep. https://doi.org/10.1038/s41598-020-74609-5 (2020). 

Scheeff S, Rivière S, Ruiz J, Abdelrahman A, Schulz-Fincke AC, Köse M, Tiburcy F, Wieczorek H, Gütschow M, Müller CE, Menche D. Synthesis of novel potent archazolids: Pharmacology of an emerging class of anticancer drugs. J Med Chem. https://doi.org/10.1021/acs.jmedchem.9b01887 (2020).

Silber N, Matos de Opitz CL, Mayer C, Sass P. Cell division protein FtsZ: from structure and mechanism to antibiotic target. Fut Microbiol. https://doi.org/10.2217/fmb-2019-0348 (2020).

Silber N, Pan S, Schäkermann S, Mayer C, Brötz-Oesterhelt H, Sass P. Cell division protein FtsZ is unfolded for N-terminal degradation by antibiotic-activated ClpP. mBio. https://doi.org/10.1128/mBio.01006-20 (2020).

Walter A, Unsleber S, Rismondo J, Jorge AM, Peschel A, Gründling A, Mayer C. Phosphoglycerol-type wall and lipoteichoic acids are enantiomeric polymers differentiated by the stereospecific glycerophosphodiesterase GlpQ. J Biol Chem. https://doi.org/10.1074/jbc.RA120.012566 (2020).

Wingen LM, Rausch M, Schneider T, Menche D. Synthesis of tetramic acid fragments derived from vancoresmycin showing inhibitory effects towards S. aureus. Chem Med Chem. https://doi.org/10.1002/cmdc.202000241 (2020).

Wingen LM, Rausch M, Schneider T, Menche D. Modular total synthesis of farnesyl analogues of cell wall precursors lipid I and II containing the Staphylococcus aureus pentaglycine bridge modification. J Org Chem. https://doi.org/10.1021/acs.joc.0c01004 (2020).

Wollnitzke P, Essig S, Gölz JP, von Schwarzenberg K, Menche D. Total synthesis of ajudazol A by a modular oxazole diversification strategy. Org Lett. https://doi.org/10.1021/acs.orglett.0c02188 (2020).

Wosniok PR, Knopf C, Dreisigacker S, Orozco-Rodriguez JM, Hinkelmann B, Müller PP, Brönstrup M, Menche D. SAR studies of the leupyrrins: Design and total synthesis of highly potent simplified leupylogs. (Honorary graphical illustration of the cover). Chemistry. https://doi.org/10.1002/chem.202002622 (2020).

 

2019

Dörr T, Moynihan PJ, Mayer C. Bacterial cell wall structure and dynamics. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2019.02051 (2019).

Macek B, Forchhammer K, Hardouin J, Weber-Ban E, Grangeasse C, Mijakovic I. Protein post-translational modifications in bacteria. Nature Reviews Microbiology. https://doi.org/10.1038/s41579-019-0243-0 (2019).

Mayer C, Sass P, Brötz-Oesterhelt H. Consequences of dosing and timing on the antibacterial effects of ADEP antibiotics. International Journal of Medical Microbiology. https://doi.org/10.1016/j.ijmm.2019.151329 (2019).

Mayer C. Peptidoglycan recycling, a promising target for antibiotic adjuvants in antipseudomonal therapy. The Journal of Infectious Diseases. https://doi.org/10.1093/infdis/jiz378 (2019).

Pan S, Malik IT, Thomy D, Henrichfreise B, Sass P. The functional ClpXP protease of Chlamydia trachomatis requires distinct clpP genes from separate genetic loci. Scientific Reports. https://doi.org/10.1038/s41598-019-50505-5 (2019).

Thomy D, Culp E, Adamek M, Cheng EY, Ziemert N, Wright GD, Sass P, Brötz-Oesterhelt H. The ADEP biosynthetic gene cluster in Streptomyces hawaiiensis NRRL 15010 reveals an accessory clpP gene as a novel antibiotic resistance factor. Applied and Environmental Microbiology, AEM-01292. https://doi.org/10.1128/AEM.01292-19 (2019). [For a free e-print, write to dhana-manon.thomyuni-tuebingen.de]