@techreport{SiegertBongaertsWagneretal.2022,
  author    = {Siegert, Petra and Bongaerts, Johannes and Wagner, Torsten and Sch{\"o}ning, Michael Josef and Selmer, Thorsten},
  title     = {Abschlussbericht zum Projekt zur {\"U}berwachung biotechnologischer Prozesse mittels Diacetyl-/Acetoin-Biosensor und Evaluierung von Acetoin-Reduktasen zur Verwendung in Biotransformationen},
  address   = {Aachen},
  organization    = {FH Aachen},
  pages     = {16 Seiten},
  year      = {2022},
  language  = {de}
}
@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{FalkenbergKohnBottetal.2023,
  author    = {Falkenberg, Fabian and Kohn, Sophie and Bott, Michael and Bongaerts, Johannes and Siegert, Petra},
  title     = {Biochemical characterisation of a novel broad pH spectrum subtilisin from Fictibacillus arsenicus DSM 15822ᵀ},
  series = {FEBS Open Bio},
  volume    = {13},
  journal   = {FEBS Open Bio},
  number    = {11},
  publisher = {Wiley},
  address   = {Hoboken, NJ},
  issn      = {2211-5463},
  doi       = {10.1002/2211-5463.13701},
  pages     = {2035 -- 2046},
  year      = {2023},
  abstract  = {Subtilisins from microbial sources, especially from the Bacillaceae family, are of particular interest for biotechnological applications and serve the currently growing enzyme market as efficient and novel biocatalysts. Biotechnological applications include use in detergents, cosmetics, leather processing, wastewater treatment and pharmaceuticals. To identify a possible candidate for the enzyme market, here we cloned the gene of the subtilisin SPFA from Fictibacillus arsenicus DSM 15822ᵀ (obtained through a data mining-based search) and expressed it in Bacillus subtilis DB104. After production and purification, the protease showed a molecular mass of 27.57 kDa and a pI of 5.8. SPFA displayed hydrolytic activity at a temperature optimum of 80 °C and a very broad pH optimum between 8.5 and 11.5, with high activity up to pH 12.5. SPFA displayed no NaCl dependence but a high NaCl tolerance, with decreasing activity up to concentrations of 5 m NaCl. The stability enhanced with increasing NaCl concentration. Based on its substrate preference for 10 synthetic peptide 4-nitroanilide substrates with three or four amino acids and its phylogenetic classification, SPFA can be assigned to the subgroup of true subtilisins. Moreover, SPFA exhibited high tolerance to 5\% (w/v) SDS and 5\% H₂O₂ (v/v). The biochemical properties of SPFA, especially its tolerance of remarkably high pH, SDS and H₂O₂, suggest it has potential for biotechnological applications.},
  language  = {en}
}
@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}
}