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

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

Software and tools

Design of mutations and smart libraries in protein engineering

Analysis of protein thermal denaturation data

Mine RiPPs and bacteriocins