Comparison of Proteomic Responses

The script works with Python 3 (3.8), matplotlib (3.3.4), numpy (1.20.1), pandas (1.2.2), scikit-learn (0.24.1), and openpyxl (3.0.6). The approach was first described in Senges CHR, Stepanek JJ, Wenzel M, Raatschen N, Ay Ü, Märtens Y, Prochnow P, Vázquez Hernández M, Yayci A, Schubert B, Janzing NBM, Warmuth HL, Kozik M, Bongard J, Alumasa JN, Albada B, Penkova M, Lukežič T, Sorto NA, Lorenz N, Miller RG, Zhu B, Benda M, Stülke J, Schäkermann S, Leichert LI, Scheinpflug K, Brötz-Oesterhelt H, Hertweck C, Shaw JT, Petković H, Brunel JM, Keiler KC, Metzler-Nolte N, Bandow JE. 2021. Comparison of proteomic responses as global approach to antibiotic mechanism of action elucidation. Antimicrob Agents Chemother 65:e01373-20. https://doi.org/10.1128/AAC.01373-20. The python script was first described in Yayci A, Schäkermann S, Berscheid A, Oesterhelt F, Miess H, Senges CHR, Gross H, Klöckner A, Schneider T, Brötz-Oesterhelt H, Bandow JE. 2021. The lipopeptide brabantamide A impairs cell envelop integrity in Gram-positive bacteria TBD. The data collected in the libraries (Excel-files) originate from a variety of publications: Bacillus subtilis: Eymann C, Homuth G, Scharf C, Hecker M. 2002 Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis. J. Bacteriol. 184:2500–2520 https://doi.org/10.1016/j.bbamem.2015.11.009 Bandow JE, Brötz H, Leichert LI, Labischinski H, Hecker M. 2003. Proteomic approach to understanding antibiotic action. 2003. Antimicrob. Agents Chemother. 47:948–955. https://doi.org/10.1128/aac.47.3.948-955.2003 Sender U, Bandow J, Engelmann S, Lindequist U, Hecker M. 2004. Proteomic signatures for daunomycin and adriamycin in Bacillus subtilis. 2004. Die Pharmazie 59:65–70 Brötz-Oesterhelt H, Beyer D, Kroll H-P, Endermann R, Ladel C, Schroeder W, Hinzen B, Raddatz S, Paulsen H, Henninger K, Bandow JE, Sahl H-G, Labischinski H. 2005. Dysregulation of bacterial proteolytic machinery by a new class of antibiotics. Nat. Med. 11, 1082–1087. https://doi.org/10.1038/nm1306 Wenzel M, Patra M, Albrecht D, Chen DY-K, Nicolaou KC, Metzler-Nolte N, Bandow JE. 2011. Proteomic signature of fatty acid biosynthesis inhibition available for in vivo mechanism-of-action studies. Antimicrob. Agents Chemother. 55:2590–2596 https://doi.org/10.1128/aac.00078-11 Wenzel M, Kohl B, Münch D, Raatschen N, Albada HB, Hamoen L, Metzler-Nolte N, Sahl H-G, Bandow JE. 2012 Proteomic response of Bacillus subtilis to lantibiotics reflects differences in interaction with the cytoplasmic membrane. Antimicrob. Agents Chemother. 56:5749–5757 https://doi.org/10.1128/aac.01380-12 Raatschen N, Wenzel M, Leichert LIO, Düchting P, Krämer U, Bandow JE. 2013. Extracting iron and manganese from bacteria with ionophores - a mechanism against competitors characterized by increased potency in environments low in micronutrients. Proteomics 13:1358–1370 https://doi.org/10.1002/pmic.201200556 Wenzel M, Patra M, Senges CHR, Ott I, Stepanek JJ, Pinto A, Prochnow P, Vuong C, Langklotz S, Metzler-Nolte N, Bandow JE. 2013. Analysis of the mechanism of action of potent antibacterial hetero-tri-organometallic compounds: a structurally new class of antibiotics. ACS chemical biology 8:1442–1450 https://doi.org/10.1021/cb4000844 Wenzel M, Chiriac AI, Otto A, Zweytick D, May C, Schumacher C, Gust R, Albada HB, Penkova M, Krämer U, Erdmann R, Metzler-Nolte N, Straus SK, Bremer E, Becher D, Brötz-Oesterhelt H, Sahl H-G, Bandow JE. 2014 Small cationic antimicrobial peptides delocalize peripheral membrane proteins. Proc. Natl. Acad. Sci. USA 111:E1409-E1418 https://doi.org/10.1073/pnas.1319900111 Münch D, Müller A, Schneider T, Kohl B, Wenzel M, Bandow JE, Maffioli S, Sosio M, Donadio S, Wimmer R, Sahl H-G. 2014. The lantibiotic NAI-107 binds to bactoprenol-bound cell wall precursors and impairs membrane functions. J. Biol. Chem. 289:12063–12076 https://doi.org/10.1074/jbc.m113.537449 Wenzel M, Senges CHR, Zhang J, Suleman S, Nguyen M, Kumar P, Chiriac AI, Stepanek JJ, Raatschen N, May C, Krämer U, Sahl H-G, Straus SK, Bandow JE. 2015. Antimicrobial peptides from the aurein family form ion-selective pores in Bacillus subtilis. ChemBioChem 16:1101–1108. https://doi.org/10.1002/cbic.201500020 Wenzel M, Schriek P, Prochnow P, Albada HB, Metzler-Nolte N, Bandow JE. 2016. Influence of lipidation on the mode of action of a small RW-rich antimicrobial peptide. BBA - Biomembranes 1858:004–1011 https://doi.org/10.1016/j.bbamem.2015.11.009 Stepanek JJ, Schäkermann S, Wenzel M, Prochnow P, Bandow JE. 2016. Purine biosynthesis is the bottleneck in trimethoprim-treated Bacillus subtilis. Proteomics. Clin. Appl. 10:1036–1048 https://doi.org/10.1002/prca.201600039 Stepanek JJ, Lukežič T, Teichert I, Petković H, Bandow JE, Dual mechanism of action of the atypical tetracycline chelocardin. 2016. BBA - Proteins and Proteomics 1864:645–654 https://doi.org/10.1016/j.bbapap.2016.03.004 Müller A, Wenzel M, Strahl H, Grein F, Saaki TNV, Kohl B, Siersma T, Bandow JE, Sahl H-G, Schneider T, Hamoen LW. 2016. Daptomycin inhibits cell envelope synthesis by interfering with fluid membrane microdomains. Proc. Natl. Acad. Sci USA 113:E7077-E7086 https://doi.org/10.1073/pnas.1611173113 Scheinpflug K, Wenzel M, Krylova O, Bandow JE, Dathe M, Strahl H. Antimicrobial peptide cWFW kills by combining lipid phase separation with autolysis. 2017. Sci. Rep. 7:44332 https://doi.org/10.1038/srep44332 Saising J, Nguyen M-T, Härtner T, Ebner P, Bhuyan AAM, Berscheid A, Muehlenkamp M, Schäkermann S, Kumari N, Maier ME, Voravuthikunchai SP, Bandow J, Lang F, Brötz-Oesterhelt H, Götz F. 2018. Rhodomyrtone (Rom) is a membrane-active compound. BBA - Biomembranes 1860:1114–1124 https://doi.org/10.1016/j.bbamem.2018.01.011 Meier D, Vázquez Hernández M, van Geelen L, Muharini R, Proksch P, Bandow JE, Kalscheuer R. 2019. The plant-derived chalcone Xanthoangelol targets the membrane of Gram-positive bacteria. Bioorg Med Chem. 27:115151 https://doi.org/10.1016/j.bmc.2019.115151 Wüllner D, Haupt A, Prochnow P, Leontiev R, Slusarenko AJ, Bandow JE. 2019 Interspecies comparison of the bacterial response to allicin reveals species-specific defense strategies. Proteomics 19:1900064(1-12). https://doi.org/10.1002/pmic.201900064 Senges CHR, Stepanek JJ, Wenzel M, Raatschen N, Ay Ü, Märtens Y, Prochnow P, Vázquez Hernández M, Yayci A, Schubert B, Janzing NBM, Warmuth HL, Kozik M, Bongard J, Alumasa JN, Albada B, Penkova M, Lukežič T, Sorto NA, Lorenz N, Miller RG, Zhu B, Benda M, Stülke J, Schäkermann S, Leichert LI, Scheinpflug K, Brötz-Oesterhelt H, Hertweck C, Shaw JT, Petković H, Brunel JM, Keiler KC, Metzler-Nolte N, Bandow JE. 2021. Comparison of proteomic responses as global approach to antibiotic mechanism of action elucidation. Antimicrob Agents Chemother 65:e01373-20. https://doi.org/10.1128/AAC.01373-20. Yayci A, Schäkermann S, Berscheid A, Oesterhelt F, Miess H, Senges CHR, Gross H, Klöckner A, Schneider T, Brötz-Oesterhelt H, Bandow JE. 2021. The lipopeptide brabantamide A impairs cell envelop integrity in Gram-positive bacteria TBD. Pseudomonas aeruginosa: Wüllner D, Haupt A, Prochnow P, Leontiev R, Slusarenko AJ, Bandow JE. 2019 Interspecies comparison of the bacterial response to allicin reveals species-specific defense strategies. Proteomics 19:1900064(1-12). https://doi.org/10.1002/pmic.201900064 Wüllner D, Thomsen J, Gesper M, Haupt A, Zhoud P, Narberhaus F, Bandow JE. 2021. Proteomic response of Pseudomonas aeruginosa to antibiotic treatment. TBD. We gratefully acknowledge funding from the German Research Foundation (BA 4193/6-1); the German Federal State of North Rhine-Westphalia for the mass spectrometer (Forschungsgroßgeräte der Länder); NRW grant Translation of Innovative Antibiotics; the German Federal State of North Rhine-Westphalia and the European Union, European Regional Development Fund, Investing in Your Future (Innovative Antibiotics from NRW and the Research Infrastructure Center for System-Based Antibiotic Research [CESAR]).