@article{PolenKraemerBongaertsetal.2005,
  author    = {Polen, T. and Kr{\"a}mer, Marco and Bongaerts, Johannes and Wubbolts, Marcel and Wendisch, V. F.},
  title     = {The global gene expression response of Escherichia coli to L-phenylalanine},
  series = {Journal of biotechnology},
  volume    = {Vol. 115},
  journal   = {Journal of biotechnology},
  number    = {Iss. 3},
  issn      = {1873-4863 (E-Journal); 0168-1656 (Print)},
  pages     = {221 -- 237},
  year      = {2005},
  language  = {en}
}
@article{BongaertsKraemerMuelleretal.2001,
  author    = {Bongaerts, Johannes and Kr{\"a}mer, Marco and M{\"u}ller, Ulrike and Raeven, Leon and Wubbolts, Marcel},
  title     = {Metabolic engineering for microbial production of aromatic amino acids and derived compounds},
  series = {Metabolic engineering},
  volume    = {Vol. 3},
  journal   = {Metabolic engineering},
  number    = {Iss. 4},
  issn      = {1096-7184 (E-Journal); 1096-7176 (Print)},
  pages     = {289 -- 300},
  year      = {2001},
  language  = {en}
}
@article{BongaertsEsserLorbachetal.2011,
  author    = {Bongaerts, Johannes and Esser, Simon and Lorbach, Volker and Al-Momani, L{\´o}ay and M{\"u}ller, Michael A. and Franke, Dirk and Grondal, Christoph and Kurutsch, Anja and Bujnicki, Robert and Takors, Ralf and Raeven, Leon and Wubbolts, Marcel and Bovenberg, Roel and Nieger, Martin and Sch{\"u}rmann, Melanie and Trachtmann, Natalie and Kozak, Stefan and Sprenger, Georg A. and M{\"u}ller, Michael},
  title     = {Diversity-oriented production of metabolites derived from chorismate and their use in organic synthesis},
  series = {Angewandte Chemie International Edition},
  volume    = {Vol. 50},
  journal   = {Angewandte Chemie International Edition},
  number    = {Iss. 34},
  publisher = {Wiley},
  address   = {Weinheim},
  issn      = {1521-3773 (E-Journal); 0570-0833 (Print); 1433-7851 (Print)},
  pages     = {7781 -- 7786},
  year      = {2011},
  language  = {en}
}
@article{MuellerBeckersMussmannetal.2018,
  author    = {M{\"u}ller, Janina and Beckers, Mario and Mußmann, Nina and Bongaerts, Johannes and B{\"u}chs, Jochen},
  title     = {Elucidation of auxotrophic deficiencies of Bacillus pumilus DSM 18097 to develop a defined minimal medium},
  series = {Microbial Cell Factories},
  volume    = {17},
  journal   = {Microbial Cell Factories},
  number    = {1},
  publisher = {BioMed Central},
  issn      = {1475-2859},
  doi       = {10.1186/s12934-018-0956-1},
  pages     = {Article No. 106},
  year      = {2018},
  abstract  = {Background Culture media containing complex compounds like yeast extract or peptone show numerous disadvantages. The chemical composition of the complex compounds is prone to significant variations from batch to batch and quality control is difficult. Therefore, the use of chemically defined media receives more and more attention in commercial fermentations. This concept results in better reproducibility, it simplifies downstream processing of secreted products and enable rapid scale-up. Culturing bacteria with unknown auxotrophies in chemically defined media is challenging and often not possible without an extensive trial-and-error approach. In this study, a respiration activity monitoring system for shake flasks and its recent version for microtiter plates were used to clarify unknown auxotrophic deficiencies in the model organism Bacillus pumilus DSM 18097. Results Bacillus pumilus DSM 18097 was unable to grow in a mineral medium without the addition of complex compounds. Therefore, a rich chemically defined minimal medium was tested containing basically all vitamins, amino acids and nucleobases, which are essential ingredients of complex components. The strain was successfully cultivated in this medium. By monitoring of the respiration activity, nutrients were supplemented to and omitted from the rich chemically defined medium in a rational way, thus enabling a systematic and fast determination of the auxotrophic deficiencies. Experiments have shown that the investigated strain requires amino acids, especially cysteine or histidine and the vitamin biotin for growth. Conclusions The introduced method allows an efficient and rapid identification of unknown auxotrophic deficiencies and can be used to develop a simple chemically defined tailor-made medium. B. pumilus DSM 18097 was chosen as a model organism to demonstrate the method. However, the method is generally suitable for a wide range of microorganisms. By combining a systematic combinatorial approach based on monitoring the respiration activity with cultivation in microtiter plates, high throughput experiments with high information content can be conducted. This approach facilitates media development, strain characterization and cultivation of fastidious microorganisms in chemically defined minimal media while simultaneously reducing the experimental effort.},
  language  = {en}
}
@article{ScheeleBongaertsMaureretal.2009,
  author    = {Scheele, S. and Bongaerts, Johannes and Maurer, K.-H. and Freudl, R.},
  title     = {Sekretion einer Kofaktor-haltigen Oxidase durch Corynebacterium glutamicum},
  series = {Chemie - Ingenieur - Technik (CIT)},
  volume    = {Vol. 81},
  journal   = {Chemie - Ingenieur - Technik (CIT)},
  number    = {Iss. 8},
  issn      = {1522-2640 (E-Journal); 0009-286X (Print)},
  pages     = {1309},
  year      = {2009},
  language  = {de}
}
@article{RachingerBauchStrittmatteretal.2013,
  author    = {Rachinger, Michael and Bauch, Melanie and Strittmatter, Axel and Bongaerts, Johannes and Evers, Stefan and Maurer, Karl-Heinz and Daniel, Rolf and Liebl, Wolfgang and Liesegang, Heiko and Ehrenreich, Armin},
  title     = {Size unlimited markerless deletions by a transconjugative plasmid-system in Bacillus licheniformis},
  series = {Journal of biotechnology},
  volume    = {Vol. 164},
  journal   = {Journal of biotechnology},
  number    = {Iss. 4},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1873-4863 (E-Journal); 0168-1656 (Print)},
  pages     = {365 -- 369},
  year      = {2013},
  language  = {en}
}
@article{WissenbachSixBongaertsetal.1995,
  author    = {Wissenbach, U. and Six, S. and Bongaerts, Johannes and Ternes, D. and Steinwachs, S. and Unden, G.},
  title     = {A third periplasmic transport system for l-arginine in Escherichia coli: molecular characterization of the artPIQMJ genes, arginine binding and transport},
  series = {Molecular microbiology},
  volume    = {Vol. 17},
  journal   = {Molecular microbiology},
  number    = {Iss. 4},
  issn      = {1365-2958 (E-Journal); 0950-382x (Print)},
  pages     = {675 -- 686},
  year      = {1995},
  language  = {en}
}
@article{HandtkeSchroeterJuergenetal.2014,
  author    = {Handtke, Stefan and Schroeter, Rebecca and J{\"u}rgen, Britta and Methling, Karen and Schl{\"u}ter, Rabea and Albrecht, Dirk and Hijum, Sacha A. F. T. van and Bongaerts, Johannes and Maurer, Karl-Heinz and Lalk, Michael and Schweder, Thomas and Hecker, Michael and Voigt, Birgit},
  title     = {Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress},
  series = {PLOS one},
  volume    = {9},
  journal   = {PLOS one},
  number    = {1},
  publisher = {PLOS},
  address   = {San Francisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0085625},
  pages     = {e85625},
  year      = {2014},
  abstract  = {Bacillus pumilus is characterized by a higher oxidative stress resistance than other comparable industrially relevant Bacilli such as B. subtilis or B. licheniformis. In this study the response of B. pumilus to oxidative stress was investigated during a treatment with high concentrations of hydrogen peroxide at the proteome, transcriptome and metabolome level. Genes/proteins belonging to regulons, which are known to have important functions in the oxidative stress response of other organisms, were found to be upregulated, such as the Fur, Spx, SOS or CtsR regulon. Strikingly, parts of the fundamental PerR regulon responding to peroxide stress in B. subtilis are not encoded in the B. pumilus genome. Thus, B. pumilus misses the catalase KatA, the DNA-protection protein MrgA or the alkyl hydroperoxide reductase AhpCF. Data of this study suggests that the catalase KatX2 takes over the function of the missing KatA in the oxidative stress response of B. pumilus. The genome-wide expression analysis revealed an induction of bacillithiol (Cys-GlcN-malate, BSH) relevant genes. An analysis of the intracellular metabolites detected high intracellular levels of this protective metabolite, which indicates the importance of bacillithiol in the peroxide stress resistance of B. pumilus.},
  language  = {en}
}
@article{MuschallikKippReckeretal.2020,
  author    = {Muschallik, Lukas and Kipp, Carina Ronja and Recker, Inga and Bongaerts, Johannes and Pohl, Martina and Gelissen, Melanie and Sch{\"o}ning, Michael Josef and Selmer, Thorsten and Siegert, Petra},
  title     = {Synthesis of α-hydroxy ketones and vicinal diols with the Bacillus licheniformis DSM 13T butane-2, 3-diol dehydrogenase},
  series = {Journal of Biotechnology},
  volume    = {202},
  journal   = {Journal of Biotechnology},
  number    = {Vol. 324},
  publisher = {Elsevier},
  address   = {Amsterdam},
  isbn      = {2590-1559},
  doi       = {10.1016/j.jbiotec.2020.09.016},
  pages     = {61 -- 70},
  year      = {2020},
  abstract  = {The enantioselective synthesis of α-hydroxy ketones and vicinal diols is an intriguing field because of the broad applicability of these molecules. Although, butandiol dehydrogenases are known to play a key role in the production of 2,3-butandiol, their potential as biocatalysts is still not well studied. Here, we investigate the biocatalytic properties of the meso-butanediol dehydrogenase from Bacillus licheniformis DSM 13T (BlBDH). The encoding gene was cloned with an N-terminal StrepII-tag and recombinantly overexpressed in E. coli. BlBDH is highly active towards several non-physiological diketones and α-hydroxyketones with varying aliphatic chain lengths or even containing phenyl moieties. By adjusting the reaction parameters in biotransformations the formation of either the α-hydroxyketone intermediate or the diol can be controlled.},
  language  = {en}
}
@article{KraemerBongaertsBovenbergetal.2003,
  author    = {Kr{\"a}mer, Marco and Bongaerts, Johannes and Bovenberg, Roel and Kremer, Susanne and M{\"u}ller, Ulrike and Orf, Sonja and Wubbolts, Marcel and Raeven, Leon},
  title     = {Metabolic engineering for microbial production of shikimic acid},
  series = {Metabolic engineering},
  volume    = {Vol. 5},
  journal   = {Metabolic engineering},
  number    = {Iss. 4},
  issn      = {1096-7184 (E-Journal); 1096-7176 (Print)},
  pages     = {277 -- 283},
  year      = {2003},
  language  = {en}
}