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Author Helge B Bode

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Towards the sustainable discovery and development of new antibiotics.

Marcus Miethke, Marco Pieroni, Tilmann Weber, Mark Brönstrup, Peter Hammann, Ludovic Halby, Paola B Arimondo, Philippe Glaser, Bertrand Aigle, Helge B Bode, Rui Moreira, Yanyan Li, Andriy Luzhetskyy, Marnix H Medema, Jean-Luc Pernodet, Marc Stadler, José Rubén Tormo, Olga Genilloud, Andrew W Truman, Kira J Weissman, Eriko Takano, Stefano Sabatini, Evi Stegmann, Heike Brötz-Oesterhelt, Wolfgang Wohlleben, Myriam Seemann, Martin Empting, Anna K H Hirsch, Brigitta Loretz, Claus-Michael Lehr, Alexander Titz, Jennifer Herrmann, Timo Jaeger, Silke Alt, Thomas Hesterkamp, Mathias Winterhalter, Andrea Schiefer, Kenneth Pfarr, Achim Hoerauf, Heather Graz, Michael Graz, Mika Lindvall, Savithri Ramurthy, Anders Karlén, Maarten van Dongen, Hrvoje Petkovic, Andreas Keller, Frédéric Peyrane, Stefano Donadio, Laurent Fraisse, Laura J V Piddock, Ian H Gilbert, Heinz E Moser, Rolf Müller,

An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of ... Read more >>

Nat Rev Chem (Nature reviews. Chemistry)
[2021, :1-24]

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Antifungal activity of different Xenorhabdus and Photorhabdus species against various fungal phytopathogens and identification of the antifungal compounds from X. szentirmaii.

Harun Cimen, Mustapha Touray, Sebnem Hazal Gulsen, Omer Erincik, Sebastian L Wenski, Helge B Bode, David Shapiro-Ilan, Selcuk Hazir,

Xenorhabdus and Photorhabdus spp. are enteric bacterial symbionts of Steinernema and Heterorhabditis nematodes, respectively. These bacteria produce an extensive set of natural products (NPs) with antibacterial, antifungal, antiprotozoal, insecticidal, or other bioactivities when vectored into insect hemocoel by nematodes. We assessed the in vitro activity of different Xenorhabdus and Photorhabdus ... Read more >>

Appl Microbiol Biotechnol (Applied microbiology and biotechnology)
[2021, 105(13):5517-5528]

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Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.

Bahar Behsaz, Edna Bode, Alexey Gurevich, Yan-Ni Shi, Florian Grundmann, Deepa Acharya, Andrés Mauricio Caraballo-Rodríguez, Amina Bouslimani, Morgan Panitchpakdi, Annabell Linck, Changhui Guan, Julia Oh, Pieter C Dorrestein, Helge B Bode, Pavel A Pevzner, Hosein Mohimani,

Nat Commun (Nature communications)
[2021, 12(1):4318]

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Synthetic Zippers as an Enabling Tool for Engineering of Non-Ribosomal Peptide Synthetases*.

Kenan A J Bozhueyuek, Jonas Watzel, Nadya Abbood, Helge B Bode,

Non-ribosomal peptide synthetases (NRPSs) are the origin of a wide range of natural products, including many clinically used drugs. Efficient engineering of these often giant biosynthetic machineries to produce novel non-ribosomal peptides (NRPs) is an ongoing challenge. Here we describe a cloning and co-expression strategy to functionally combine NRPS fragments ... Read more >>

Angew Chem Int Ed Engl (Angewandte Chemie (International ed. in English))
[2021, 60(32):17531-17538]

Cited: 1 time

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Climate-specific biosynthetic gene clusters in populations of a lichen-forming fungus.

Garima Singh, Anjuli Calchera, Meike Schulz, Moritz Drechsler, Helge B Bode, Imke Schmitt, Francesco Dal Grande,

Natural products can contribute to abiotic stress tolerance in plants and fungi. We hypothesize that biosynthetic gene clusters (BGCs), the genomic elements that underlie natural product biosynthesis, display structured differences along elevation gradients. We analysed biosynthetic gene variation in natural populations of the lichen-forming fungus Umbilicaria pustulata. We collected a ... Read more >>

Environ Microbiol (Environmental microbiology)
[2021, 23(8):4260-4275]

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Structure and biosynthesis of deoxy-polyamine in Xenorhabdus bovienii.

Sebastian L Wenski, Natalie Berghaus, Nadine Keller, Helge B Bode,

Polyamine moieties have been described as part of the fabclavine and zeamine family of natural products. While the corresponding biosynthetic gene clusters have been found in many different proteobacteria, a unique BGC was identified in the entomopathogenic bacterium Xenorhabdus bovienii. Mass spectrometric analysis of a X. bovienii mutant strain revealed ... Read more >>

J Ind Microbiol Biotechnol (Journal of industrial microbiology & biotechnology)
[2021, 48(3-4):]

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Xenocoumacin 2 reduces protein biosynthesis and inhibits inflammatory and angiogenesis-related processes in endothelial cells.

Pelin Erkoc, Michaela Schmitt, Rebecca Ingelfinger, Iris Bischoff-Kont, Larissa Kopp, Helge B Bode, Susanne Schiffmann, Robert Fürst,

Xenocoumacin (Xcn) 1 and 2 are the major antibiotics produced by the insect-pathogenic bacterium Xenorhabdus nematophila. Although the antimicrobial activity of Xcns has been explored, research regarding their action on mammalian cells is lacking. We aimed to investigate the action of Xcns in the context of inflammation and angiogenesis. We ... Read more >>

Biomed Pharmacother (Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie)
[2021, 140:111765]

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Relative potency of a novel acaricidal compound from Xenorhabdus, a bacterial genus mutualistically associated with entomopathogenic nematodes.

Gamze Incedayi, Harun Cimen, Derya Ulug, Mustapha Touray, Edna Bode, Helge B Bode, Esra Orenlili Yaylagul, Selcuk Hazir, Ibrahim Cakmak,

Our study aimed to identify the novel acaricidal compound in Xenorhabdus szentirmaii and X. nematophila using the easyPACId approach (easy Promoter Activated Compound Identification). We determined the (1) effects of cell-free supernatant (CFS) obtained from mutant strains against T. urticae females, (2) CFS of the acaricidal bioactive strain of X. ... Read more >>

Sci Rep (Scientific reports)
[2021, 11(1):11253]

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Cooperation between a T Domain and a Minimal C-Terminal Docking Domain to Enable Specific Assembly in a Multiprotein NRPS.

Jonas Watzel, Elke Duchardt-Ferner, Sepas Sarawi, Helge B Bode, Jens Wöhnert,

Non-ribosomal peptide synthetases (NRPS) produce natural products from amino acid building blocks. They often consist of multiple polypeptide chains which assemble in a specific linear order via specialized N- and C-terminal docking domains (<sup>N/C</sup> DDs). Typically, docking domains function independently from other domains in NRPS assembly. Thus, docking domain replacements ... Read more >>

Angew Chem Int Ed Engl (Angewandte Chemie (International ed. in English))
[2021, 60(25):14171-14178]

Cited: 1 time

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A Desaturase-Like Enzyme Catalyzes Oxazole Formation in Pseudomonas Indolyloxazole Alkaloids.

Alexander O Brachmann, Silke I Probst, Joel Rüthi, Darya Dudko, Helge B Bode, Jörn Piel,

Indolyloxazole alkaloids occur in diverse micro- and macroorganisms and exhibit a wide range of pharmacological activities. Despite their ubiquitous occurrence and simple structures, the biosynthetic pathway remained unknown. Here, we used transposon mutagenesis in the labradorin producer Pseudomonas entomophila to identify a cryptic biosynthetic locus encoding an N-acyltransferase and a ... Read more >>

Angew Chem Int Ed Engl (Angewandte Chemie (International ed. in English))
[2021, 60(16):8781-8785]

Cited: 2 times

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Microbial Cationic Peptides as a Natural Defense Mechanism against Insect Antimicrobial Peptides.

Tien Duy Vo, Christoph Spahn, Mike Heilemann, Helge B Bode,

Bacteria produce a plethora of specialized metabolites (SM), with the ecological function of most of them not known. A major group of SM are peptides derived from nonribosomal peptide synthetases (NRPS). In entomopathogenic bacteria of the genus <i>Xenorhabdus</i>, PAX (peptide-antimicrobial-<i>Xenorhabdus</i>) were described as NRPS-derived lipopeptides, which show antimicrobial activities against ... Read more >>

ACS Chem Biol (ACS chemical biology)
[2021, 16(3):447-451]

Cited: 1 time

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NMR resonance assignments for a docking domain pair with an attached thiolation domain from the PAX peptide-producing NRPS from Xenorhabdus cabanillasii.

Jonas Watzel, Sepas Sarawi, Elke Duchardt-Ferner, Helge B Bode, Jens Wöhnert,

Non-ribosomal peptide synthetases (NRPSs) are large multienzyme machineries. They synthesize numerous important natural products starting from amino acids. For peptide synthesis functionally specialized NRPS modules interact in a defined manner. Individual modules are either located on a single or on multiple different polypeptide chains. The "peptide-antimicrobial-Xenorhabdus" (PAX) peptide producing NRPS ... Read more >>

Biomol NMR Assign (Biomolecular NMR assignments)
[2021, 15(1):229-234]

Cited: 1 time

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Photorhabdus heterorhabditis subsp. aluminescens subsp. nov., Photorhabdus heterorhabditis subsp. heterorhabditis subsp. nov., Photorhabdus australis subsp. thailandensis subsp. nov., Photorhabdus australis subsp. australis subsp. nov., and Photorhabdus aegyptia sp. nov. isolated from Heterorhabditis entomopathogenic nematodes.

Ricardo A R Machado, Arthur Muller, Shimaa M Ghazal, Aunchalee Thanwisai, Sylvie Pagès, Helge B Bode, Mona A Hussein, Kamal M Khalil, Louis S Tisa,

Three Gram-stain-negative, rod-shaped, non-spore-forming bacteria, BA1<sup>T</sup>, Q614<sup>T</sup> and PB68.1<sup>T</sup>, isolated from the digestive system of <i>Heterorhabditis</i> entomopathogenic nematodes, were biochemically and molecularly characterized to clarify their taxonomic affiliations. The 16S rRNA gene sequences of these strains suggest that they belong to the Gammaproteobacteria, to the family <i>Morganellacea</i>, and to the ... Read more >>

Int J Syst Evol Microbiol (International journal of systematic and evolutionary microbiology)
[2021, 71(1):]

Cited: 1 time

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Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.

Alison E Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T Konstantinidis, Christopher E Lane, R Thane Papke, Donovan H Parks, Ramon Rossello-Mora, Matthew B Stott, Iain C Sutcliffe, J Cameron Thrash, Stephanus N Venter, William B Whitman, Silvia G Acinas, Rudolf I Amann, Karthik Anantharaman, Jean Armengaud, Brett J Baker, Roman A Barco, Helge B Bode, Eric S Boyd, Carrie L Brady, Paul Carini, Patrick S G Chain, Daniel R Colman, Kristen M DeAngelis, Maria Asuncion de Los Rios, Paulina Estrada-de Los Santos, Christopher A Dunlap, Jonathan A Eisen, David Emerson, Thijs J G Ettema, Damien Eveillard, Peter R Girguis, Ute Hentschel, James T Hollibaugh, Laura A Hug, William P Inskeep, Elena P Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G Lloyd, Frank E Löffler, Thulani P Makhalanyane, Duane P Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedrós-Alió, Alexander J Probst, Theo H M Smits, Andrew D Steen, Emma T Steenkamp, Anja Spang, Frank J Stewart, James M Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Pablo Yarza, Brian P Hedlund, Anna-Louise Reysenbach,

Nat Microbiol (Nature microbiology)
[2021, 6(1):136]

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Symbiosis, virulence and natural-product biosynthesis in entomopathogenic bacteria are regulated by a small RNA.

Nick Neubacher, Nicholas J Tobias, Michaela Huber, Xiaofeng Cai, Timo Glatter, Sacha J Pidot, Timothy P Stinear, Anna Lena Lütticke, Kai Papenfort, Helge B Bode,

Photorhabdus and Xenorhabdus species have mutualistic associations with nematodes and an entomopathogenic stage<sup>1,2</sup> in their life cycles. In both stages, numerous specialized metabolites are produced that have roles in symbiosis and virulence<sup>3,4</sup>. Although regulators have been implicated in the regulation of these specialized metabolites<sup>3,4</sup>, how small regulatory RNAs (sRNAs) are ... Read more >>

Nat Microbiol (Nature microbiology)
[2020, 5(12):1481-1489]

Cited: 1 time

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Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host.

Abigail M D Maher, Mohamed Asaiyah, Sarajane Quinn, Riona Burke, Hendrik Wolff, Helge B Bode, Christine T Griffin,

Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building ... Read more >>

Microb Ecol (Microbial ecology)
[2021, 81(1):223-239]

Cited: 1 time

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Cell-Free Synthesis of Natural Compounds from Genomic DNA of Biosynthetic Gene Clusters.

Ilka Siebels, Sarah Nowak, Christina S Heil, Peter Tufar, Niña S Cortina, Helge B Bode, Martin Grininger,

A variety of chemicals can be produced in a living host cell via optimized and engineered biosynthetic pathways. Despite the successes, pathway engineering remains demanding because of the lack of specific functions or substrates in the host cell, the cell's sensitivity in vital physiological processes to the heterologous components, or ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2020, 9(9):2418-2426]

Cited: 2 times

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Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis.

Alois Bräuer, Qiuqin Zhou, Gina L C Grammbitter, Maximilian Schmalhofer, Michael Rühl, Ville R I Kaila, Helge B Bode, Michael Groll,

Type II polyketide synthases (PKSs) are multi-enzyme complexes that produce secondary metabolites of medical relevance. Chemical backbones of such polyketides are produced by minimal PKS systems that consist of a malonyl transacylase, an acyl carrier protein and an α/β heterodimeric ketosynthase. Here, we present X-ray structures of all ternary complexes ... Read more >>

Nat Chem (Nature chemistry)
[2020, 12(8):755-763]

Cited: 3 times

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Roadmap for naming uncultivated Archaea and Bacteria.

Alison E Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T Konstantinidis, Christopher E Lane, R Thane Papke, Donovan H Parks, Ramon Rossello-Mora, Matthew B Stott, Iain C Sutcliffe, J Cameron Thrash, Stephanus N Venter, William B Whitman, Silvia G Acinas, Rudolf I Amann, Karthik Anantharaman, Jean Armengaud, Brett J Baker, Roman A Barco, Helge B Bode, Eric S Boyd, Carrie L Brady, Paul Carini, Patrick S G Chain, Daniel R Colman, Kristen M DeAngelis, Maria Asuncion de Los Rios, Paulina Estrada-de Los Santos, Christopher A Dunlap, Jonathan A Eisen, David Emerson, Thijs J G Ettema, Damien Eveillard, Peter R Girguis, Ute Hentschel, James T Hollibaugh, Laura A Hug, William P Inskeep, Elena P Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G Lloyd, Frank E Löffler, Thulani P Makhalanyane, Duane P Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedrós-Alió, Alexander J Probst, Theo H M Smits, Andrew D Steen, Emma T Steenkamp, Anja Spang, Frank J Stewart, James M Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Pablo Yarza, Brian P Hedlund, Anna-Louise Reysenbach,

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ... Read more >>

Nat Microbiol (Nature microbiology)
[2020, 5(8):987-994]

Cited: 19 times

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Nonribosomal Peptides Produced by Minimal and Engineered Synthetases with Terminal Reductase Domains.

Andreas Tietze, Yan-Ni Shi, Max Kronenwerth, Helge B Bode,

Nonribosomal peptide synthetases (NRPSs) use terminal reductase domains for 2-electron reduction of the enzyme-bound thioester releasing the generated peptides as C-terminal aldehydes. Herein, we reveal the biosynthesis of a pyrazine that originates from an aldehyde-generating minimal NRPS termed ATRed in entomopathogenic Xenorhabdus indica. Reductase domains were also investigated in terms ... Read more >>

Chembiochem (Chembiochem : a European journal of chemical biology)
[2020, 21(19):2750-2754]

Cited: 3 times

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Artificial Splitting of a Non-Ribosomal Peptide Synthetase by Inserting Natural Docking Domains.

Carsten Kegler, Helge B Bode,

The interaction in multisubunit non-ribosomal peptide synthetases (NRPSs) is mediated by docking domains that ensure the correct subunit-to-subunit interaction. We introduced natural docking domains into the three-module xefoampeptide synthetase (XfpS) to create two to three artificial NRPS XfpS subunits. The enzymatic performance of the split biosynthesis was measured by absolute ... Read more >>

Angew Chem Int Ed Engl (Angewandte Chemie (International ed. in English))
[2020, 59(32):13463-13467]

Cited: 5 times

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Fabclavine diversity in Xenorhabdus bacteria.

Sebastian L Wenski, Harun Cimen, Natalie Berghaus, Sebastian W Fuchs, Selcuk Hazir, Helge B Bode,

The global threat of multiresistant pathogens has to be answered by the development of novel antibiotics. Established antibiotic applications are often based on so-called secondary or specialized metabolites (SMs), identified in large screening approaches. To continue this successful strategy, new sources for bioactive compounds are required, such as the bacterial ... Read more >>

Beilstein J Org Chem (Beilstein journal of organic chemistry)
[2020, 16:956-965]

Cited: 2 times

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A New Docking Domain Type in the Peptide-Antimicrobial-Xenorhabdus Peptide Producing Nonribosomal Peptide Synthetase from Xenorhabdus bovienii.

Jonas Watzel, Carolin Hacker, Elke Duchardt-Ferner, Helge B Bode, Jens Wöhnert,

Nonribosomal peptide synthetases (NRPSs) produce a wide variety of different natural products from amino acid precursors. In contrast to single protein NRPS, the NRPS of the bacterium <i>Xenorhabdus bovienii</i> producing the peptide-antimicrobial-Xenorhabdus (PAX) peptide consists of three individual proteins (PaxA/B/C), which interact with each other noncovalently in a linear fashion. ... Read more >>

ACS Chem Biol (ACS chemical biology)
[2020, 15(4):982-989]

Cited: 5 times

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Publisher Correction: Engineering bacterial symbionts of nematodes improves their biocontrol potential to counter the western corn rootworm.

Ricardo A R Machado, Lisa Thönen, Carla C M Arce, Vanitha Theepan, Fausto Prada, Daniel Wüthrich, Christelle A M Robert, Evangelia Vogiatzaki, Yi-Ming Shi, Olivier P Schaeren, Matheus Notter, Rémy Bruggmann, Siegfried Hapfelmeier, Helge B Bode, Matthias Erb,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Biotechnol (Nature biotechnology)
[2020, 38(5):649]

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Phototemtide A, a Cyclic Lipopeptide Heterologously Expressed from Photorhabdus temperata Meg1, Shows Selective Antiprotozoal Activity.

Lei Zhao, Tien Duy Vo, Marcel Kaiser, Helge B Bode,

A new cyclic lipopeptide, phototemtide A (1), was isolated from Escherichia coli expressing the biosynthetic gene cluster pttABC from Photorhabdus temperata Meg1. The structure of 1 was elucidated by HR-ESI-MS and NMR experiments. The absolute configurations of amino acids and 3-hydroxyoctanoic acid in 1 were determined by using the advanced Marfey's ... Read more >>

Chembiochem (Chembiochem : a European journal of chemical biology)
[2020, 21(9):1288-1292]

Cited: 3 times

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