Project publications

  • The contribution of bacterial genome engineering to sustainable development Reuß D, Commichau F, Stülke J. Microbial Biotechnology 2017 vol: 10 (5) pp: 1259-1263 DOI 10.1111/1751-7915.12784

  • Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology Dvořák P, Nikel P, Damborský J, de Lorenzo V. Biotechnology Advances 2017 vol: 35 (7) pp: 845-866 DOI 10.1016/J.BIOTECHADV.2017.08.001

  • BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins van Heel A, de Jong A, Song C, Viel J, Kok J et. al. Nucleic Acids Research 2018 vol: 46 (W1) pp: W278-W281 DOI 10.1093/nar/gky383

  • Less is more: towards a genome-reduced Bacillus cell factory for ‘difficult proteins’ Aguilar Suarez R, Stülke J, van Dijl J, ACS Synthetic Biology, 2018 DOI 10.1021/acssynbio.8b00342

  • Microbial cell factories for the sustainable manufacturing of B vitamins Acevedo-Rocha C, Gronenberg L, Mack M, Commichau F, Genee H. Current Opinion in Biotechnology 2019 vol: 56 pp: 18-29 DOI 10.1016/J.COPBIO.2018.07.006

  • Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories van Tilburg A, Cao H, van der Meulen S, Solopova A, Kuipers O Current Opinion in Biotechnology 2019 vol: 59 pp: 1-7 DOI 10.1016/J.COPBIO.2019.01.007

  • A survey of pyridoxal 5’-phosphate-dependent proteins in the Gram-positive model bacterium Bacillus subtilis Commichau F, Richts B, Rosenberg J Frontiers in Molecular Biosciences 2019 vol: 6 pp: 32 DOI 10.3389/FMOLB.2019.00032

  • Resistance to serine in Bacillus subtilis: Identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism Klewing A, Mo Koo B, Krüger L, Poehlein A, Reuß D, Daniel R, Gross C.A., Stülke J

  • Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis Benda M, Woelfel S, Gunka K, Klumpp S, Poehlein A, Kálalová D, Šanderová H, Daniel R, Krásný L, Stülke J bioRxiv 2020.05.20.106237; doi: https://doi.org/10.1101/2020.05.20.106237

  • EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities Hon J, Borko S, Stourac J, Prokop Z, Zendulka J, Bednar D, Martinek T, Damborsky J 2020 Nucleic Acids Research, gkaa372, https://doi.org/10.1093/nar/gkaa372   

  • MiniBacillus PG10 as a convenient and effective production host for lantibiotics van Tilburg A, van Heel A, Stülke J, de Kok N, Rueff AS, Kuipers O ACS Synthetic Biology June 2020 DOI: https://doi.org/10.1021/acssynbio.0c00194

Other relevant publications from our partners

  • Exploring the Existence of Lipid Rafts in Bacteria Bramkamp M, Lopez D Microbiology and Molecular Biology Reviews 2015 vol: 79 (1) pp: 81-100 DOI: 10.1128/MMBR.00036-14

  • Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species Zhao X, Kuipers O BMC Genomics 2016 vol: 17 (1) pp: 882 DOI: 10.1186/s12864-016-3224-y

  • Discovery, Production and Modification of Five Novel Lantibiotics Using the Promiscuous Nisin Modification Machinery van Heel A, Kloosterman T, Montalban-Lopez M, Deng J, Plat A et. al. ACS Synthetic Biolog2016 vol: 5 (10) pp: 1146-1154 DOI: 10.1021/acssynbio.6b00033

  • Membrane Microdomain Disassembly Inhibits MRSA Antibiotic Resistance García-Fernández E, Koch G,Wagner R, Fekete A, Stengel S et. al. Cell 2017 vol: 171 (6) pp: 1354-1367.e20 DOI 10.1016/j.cell.2017.10.012

  • Genome-guided identification of novel head-to-tail cyclized antimicrobial peptides, exemplified by the discovery of pumilarin van Heel A, Montalban-Lopez M, Oliveau Q, Kuipers O Microbial genomics 2017 vol: 3 (10) pp: e000134 DOI: 10.1099/mgen.0.000134

  • Major gene-regulatory mechanisms operating in ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthesis Bartholomae M, Buivydas A, Viel J, Montalbán-López M, Kuipers O Molecular Microbiology 2017 vol: 106 (2) pp: 186-206 DOI: 10.1111/mmi.13764

  • Mining prokaryotes for antimicrobial compounds: from diversity to function Tracanna V, de Jong A, Medema M, Kuipers O FEMS Microbiology Reviews 2017 vol: 41 (3) pp: 417-429 DOI: 10.1093/femsre/fux014 

  • Cell surface engineering of Bacillus subtilis improves production yields of heterologously expressed α-amylases. Cao H, van Heel A, Ahmed H, Mols M, Kuipers O Microbial Cell Factories 2017 vol: 16 (1) pp: 56 DOI: 10.1186/s12934-017-0674-0

  • Employing the promiscuity of lantibiotic biosynthetic machineries to produce novel antimicrobials Montalbán-López M, van Heel A, Kuipers O FEMS Microbiology Reviews 2017 vol: 41 (1) pp: 5-18 DOI: 10.1093/femsre/fuw034 

  • Fluorescently Labeled DNA Interacts with Competence and Recombination Proteins and Is Integrated and Expressed Following Natural Transformation of Bacillus subtilis Boonstra M, Vesel N, Kuipers O. mBio 2018 vol: 9 (5) pp: e01161-18 DOI: 10.1128/mBio.01161-18

  • Increasing the Antimicrobial Activity of Nisin-Based Lantibiotics against Gram-Negative Pathogens Li Q, Montalban-Lopez M, Kuipers O, Applied and environmental microbiology2018 vol: 84 (12) pp: e00052-18 DOI: 10.1128/AEM.00052-18 

  • A two-step evolutionary process establishes a non-native vitamin B6 pathway in Bacillus subtilis Rosenberg J, Yeak K, Commichau F. Environmental Microbiology 2018 vol: 20 (1) pp: 156-168 DOI 10.1111/1462-2920.13950

  • Harnessing Underground Metabolism for Pathway Development. Rosenberg J, Commichau F. Trends in biotechnology 2018 vol: 0 (0) DOI10.1016/j.tibtech.2018.08.001

  • Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips Pilát Z, Kizovský M, Ježek J, Krátký S, Sobota J et. al. Sensors 2018 vol: 18 (10) pp: 3212 DOI: 10.3390/s18103212

  • Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site Kokkonen P, Bednar D, Dockalova V, Prokop Z, Damborsky J Journal of Biological Chemistry 2018 vol: 293 (29) pp: 11505-11512 DOI: 10.1074/jbc.RA117.000328

  • Viscosity solutions to evolution problems of star-shaped reachable sets Mazurenko S Nonlinear Differential Equations and Applications NoDEA 2018 vol: 25 (4) pp: 29 DOI: 10.1007/s00030-018-0516-8

  • Sensitive operation of enzyme-based biodevices by advanced signal processing Mazurenko S, Bidmanova S, Kotlanova M, Damborsky J, Prokop Z
    PLOS ONE 2018 vol: 13 (6) pp: e0198913 DOI: 10.1371/journal.pone.0198913

  • Haloalkane Dehalogenases From Marine Organisms Kunka A, Damborsky J, Prokop Z Methods in Enzymology 2018 vol: 605 pp: 203-251 DOI: 10.1016/BS.MIE.2018.03.005

  • CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. Jurcik A, Bednar D, Byska J, Marques S, Furmanova K et. al. Bioinformatics (Oxford, England) 2018 vol: 34 (20) pp: 3586-3588 DOI: 10.1093/bioinformatics/bty386

  • Impact of the access tunnel engineering on catalysis is strictly ligand-specific Kaushik S, Marques S, Khirsariya P, Paruch K, Libichova L et. al. The FEBS Journal 2018 vol: 285 (8) pp: 1456-1476 DOI: 10.1111/febs.14418
  • Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization Vanacek P, Sebestova E, Babkova P, Bidmanova S, Daniel L et. al. ACS Catalysis 2018 vol: 8 (3) pp: 2402-2412 DOI: 10.1021/acscatal.7b03523
  • Computer-assisted engineering of hyperstable fibroblast growth factor 2 Dvorak P, Bednar D, Vanacek P, Balek L, Eiselleova L et. al. Biotechnology and Bioengineering 2018 vol: 115 (4) pp: 850-862 DOI: 10.1002/bit.26531
  • Gram-scale production of recombinant microbial enzymes in shake flasks Chrast L, Chaloupkova R, Damborsky J FEMS Microbiology Letters 2018 vol: 365 (2) DOI: 10.1093/femsle/fnx265
  • A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity Buryska T, Babkova P, Vavra O, Damborsky J, Prokop Z, Applied and Environmental Microbiology 2017 vol: 84 (2) DOI: 10.1128/AEM.01684-17
  • CalFitter: a web server for analysis of protein thermal denaturation data Mazurenko S, Stourac J, Kunka A, Nedeljković S, Bednar D et. al. Nucleic Acids Research 2018 vol: 46 (W1) pp: W344-W349 DOI 10.1093/nar/gky358
  • HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information Sumbalova L, Stourac J, Martinek T, Bednar D, Damborsky J, Nucleic Acids Research 2018 gky417.
  • Haloalkane Dehalogenases From Marine Organisms Kunka A, Damborsky J, Prokop Z. Methods in Enzymology 2018 605: 203-251.  DOI 10.1016/bs.mie.2018.03.005
  • Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization Beerens K, Mazurenko S, Kunka A ,Marques S, Hansen N et. al. ACS Catalysis 2018 vol: 8 (10) pp: 9420-9428 DOI: 10.1021/acscatal.8b01677

  • Microbial cell factories for the sustainable manufacturing of B vitamins Acevedo-Rocha C, Gronenberg L, Mack M, Commichau F, Genee H. Current Opinion in Biotechnology 2019 vol: 56 pp: 18-29 DOI 10.1016/J.COPBIO.2018.07.006

  • Decoupling of recombinant protein production from Escherichia coli cell growth enhances functional expression of plant Leloir glycosyltransferases. Lemmerer M, Mairhofer J, Lepak A, Longus K, Hahn R et. al. Biotechnology and Bioengineering 2019 pp: bit.26934 DOI10.1002/bit.26934

  • Heterologous biosynthesis and characterization of a glycocin from a thermophilic bacterium Kaunietis A, Buivydas A, Čitavičius D, Kuipers O Nature Communications 2019 vol: 10 (1) pp: 1115 DOI: 10.1038/s41467-019-09065-5

  • Development of Fluorescent Assay for Monitoring of Dehalogenase Activity Nevolova S, Manaskova E, Mazurenko S, Damborsky J, Prokop Z Biotechnology Journal 2019 vol: 14 (3) pp: 1800144 DOI: 10.1002/biot.201800144

  • Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase. Jindal G, Slanska K, Kolev V, Damborsky J, Prokop Z et. al. Proceedings of the National Academy of Sciences of the United States of America 2019 vol: 116 (2) pp: 389-394 DOI: 10.1073/pnas.1804979115

  • Computational Study of Protein-Ligand Unbinding for Enzyme Engineering Marques S, Bednar D, Damborsky J Frontiers in Chemistry 2019 vol: 6 pp: 650 DOI: 10.3389/fchem.2018.00650 

  • Fluorescent pH Indicators for Neutral to Near-Alkaline Conditions Based on 9-Iminopyronin Derivatives Horváth P, Šebej P, Kovář D, Damborský J, Prokop Z et. al. ACS Omega 2019 vol: 4 (3) pp: 5479-5485 DOI: 10.1021/acsomega.9b00362

  • Computational Design of Stable and Soluble Biocatalysts Musil M, Konegger H, Hon J, Bednar D, Damborsky J ACS Catalysis 2019 vol: 9 (2) pp: 1033-1054 DOI: 10.1021/acscatal.8b03613

  • Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis. Reuß DR, Faßhauer P, Mroch PJ, Ul-Haq I, Koo BM, Pöhlein A, Gross CA, Daniel R, Brantl S, Stülke J Nucleic Acids Res 2019 47, 5231–5242  DOI: 10.1093/nar/gkz260 

  • Machine Learning in Enzyme Engineering  Mazurenko S, Prokop Z, Damborsky J ACS Catal. 2020, 10, 2, 1210-1223 DOI 10.1021/acscatal.9b04321

  • Bacteriophage Inspired Growth-Decoupled Recombinant Protein Production in Escherichia coli Stargardt P, Feuchtenhofer L, Cserjan-Puschmann M, Striedner G, Mairhofer J ACS Synth. Biol. 2020 DOI: 10.1021/acssynbio.0c00028

Software and tools

Design of mutations and smart libraries in protein engineering

Analysis of protein thermal denaturation data

Mine RiPPs and bacteriocins

Automated mining of soluble enzymes

Prediction of soluble protein expression in E. coli.