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

  • 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.

  • 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

  • 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

  • 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 factorie 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

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 Biology 2016 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 microbiology 2018 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

  • 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

Software and tools

Design of mutations and smart libraries in protein engineering

Analysis of protein thermal denaturation data

Mine RiPPs and bacteriocins