Publications, Projects
& Major presentations
Flagship Publications
Dvořák P, Burýšková B, Popelářová B, Ebert BE, Botka T, Bujdoš D, Sánchez-Pascuala A, Schöttler H, Hayen H, de Lorenzo V, Blank LM, Benešík M. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nature Communications 2024,15(1):2666. doi: 10.1038/s41467-024-46812-9
In this work, we decide on quality over quantity and we provide an in-depth analysis of two lineages of bacterial strains of Pseudomonas putida engineered and evolved in parallel toward better growth on abundant sugar D-xylose found in waste plant biomass. The findings are important for better designs of microbial cell factories for the valorization of lignocellulosic waste as well as for better understanding of bacterial adaptation to non-native substrates.
Bujdoš D, Popelářová B, Volke DC, Nikel P, Sonnenschein N, Dvořák P. Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model. Metabolic Engineering 2023, 75:29-46. doi: https://doi.org/10.1016/j.ymben.2022.10.011
In this study, authored by Dalimil and co-authored by Barča, we introduce a novel strategy for aerobic overproduction of important metabolic precursor of many useful chemicals - pyruvate - in bacterial cells. We also present an upgraded version of the genome-scale metabolic model of our favourite microbial host Pseudomonas putida.
Dvořák P, Kováč J, de Lorenzo V. Biotransformation of D-xylose to D-xylonate coupled to medium-chain-length polyhydroxyalkanoate production in cellobiose-grown Pseudomonas putida EM42. Microbial Biotechnology 2020, 13(4):1273-83. doi: https://doi.org/10.1111/1751-7915.13574
In this work, we demonstrate the ability of Pseudomonas putida EM42 to simultaneously valorize two important lignocellulosic sugars by converting them into the platform chemical D-xylonate and medium-chain-length polyhydroxyalkanoates (mcl PHA). This study not only showcases the versatility of P. putida EM42 as a microbial platform but also introduces cellobiose as a novel substrate for mcl PHA production.
Dvořák P, Bayer EA, de Lorenzo V. Surface display of designer protein scaffolds on genome-reduced strains of Pseudomonas putida. ACS Synthetic Biology 2020, 9(10):2749–64. doi: https://doi.org/10.1021/acssynbio.0c00276
In this study, we report an essential step in building biocatalytic scaffolds on bacteria - a display of designer enzyme-anchoring protein “scaffoldins” on the surface of Pseudomonas putida. Our results highlight the value of cell surface engineering for the presentation of recombinant proteins on the envelope of G- bacteria.
2024 Publications
23) Dvořák P, Burýšková B, Popelářová B, Ebert BE, Botka T, Bujdoš D, Sánchez-Pascuala A, Schöttler H, Hayen H, de Lorenzo V, Blank LM, Benešík M. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nature Communications 2024,15(1):2666. doi: 10.1038/s41467-024-46812-9
Previous publications, major presentations and projects
Year 2023
PUBLICATIONS:
22) Musilova J, Kourilova X, Hermankova K, Bezdicek M, Ieremenko A, Dvorak P, Obruca S, Sedlar K. Genomic and Phenotypic Comparison of Polyhydroxyalkanoates Producing Strains of Genus Caldimonas/Schlegelella. Computational and Structural Biotechnology 2023, 21:5372-5381. doi: https://doi.org/10.1016/j.csbj.2023.10.051
21) Dvořák P, Galvão TC, Pflüger-Grau K, Banks AM, de Lorenzo V, Jiménez JI. Water potential governs the effector specificity of the transcriptional regulator XylR of Pseudomonas putida. Environmental Microbiology 2023, 25:1041-1054. doi: https://doi.org/10.1111/1462-2920.16342
20) Bujdoš D, Popelářová B, Volke DC, Nikel P, Sonnenschein N, Dvořák P. Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model. Metabolic Engineering 2023, 75:29-46. doi: https://doi.org/10.1016/j.ymben.2022.10.011
PRESENTATIONS:
Barbora Burýšková presented a talk entitled "Mutualistic bacterial consortium for the co-utilisation of lignocellulosic disaccharides" at GASB and Designer Biology Conference 2023, Freiburg im Breisgau, Germany (19.9.2023).
Anastasiia Ieremenko presented a talk entitled "Developing a Genetic Manipulation Toolkit for Caldimonas thermodepolymerans" at the European Symposium on Biopolymers 2023, Brno, Czech Republic (13.9.2023).
Barbora Hrnčířová presented a talk entitled "Unlocking the potential of inedible plant biomass using microbial engineering and synthetic biology" at NATO STO Early Career Scientist Event 2023, Espoo, Finland (21.9.2023).
Pavel Dvořák presented a talk entitled "PUSH-based Strategy to Increase Glycolytic Flux in Pseudomonas putida from co-Utilized Cellulosic Sugars to Biopolymer Precursors" at the European Symposium on Biopolymers 2023, Brno, Czech Republic (13.9.2023).
Pavel Dvořák presented a talk entitled "Upgrading Pseudomonas putida by systems metabolic engineering for lignocellulose biotechnology" at FEMS Congress 2023, Hamburg, Germany (11.7.2023).
Pavel Dvořák presented a talk entitled "Upgrading Pseudomonas putida by systems metabolic engineering for biotechnological processing of lignocellulosic sugars. " at Metabolic Engineering 15, Singapore 2023 (11.6.2023).
Year 2022
PUBLICATIONS:
19) Juračka S, Hrnčířová B, Burýšková B, Georgiev D, Dvořák P. Building the SynBio community in the Czech Republic from the bottom up: You get what you give. Biotechnology Notes 2022, 3:124-134. doi: https://doi.org/10.1016/j.biotno.2022.11.002
18) Martinez-Garcia E, Fraile S, Algar Parejo E, Aparicio T, Velázquez Muñoz E, Calles B, Tas H, Blázquez B, Martin B, Prieto Hernández C, Sánchez-Sampedro L, Nørholm M, Volke D, Wirth N, Dvořák P, Alejaldre L, Grozinger L, Crowther M, Goni-Moreno A, Nikel PI, Nogales J, de Lorenzo V. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Research 2022, gkac1059. doi: https://doi.org/10.1093/nar/gkac1059
17) Obruča S, Dvořák P, Sedláček P, Koller M, Sedlář K, Pernicová I, Šafránek D. Polyhydroxyalkanoates synthesis by halophiles and thermophiles: towards sustainable production of microbial bioplastics. Biotechnology Advances 2022, 58:107906. https://doi.org/10.1016/j.biotechadv.2022.107906
PROJECTS:
2022-2024: Grant Agency of Masaryk University (GAMU), Masaryk Award in Science and Humanities (MASH) Junior. A new generation bacterial platform for lignocellulose biotechnology; principal investigator Pavel Dvořák
2022-2024: Czech Science Foundation (GAČR), Standard project GA22-12505S; principal investigator Pavel Dvořák
2022-2024: Czech Science Foundation (GAČR), Standard project GA22-10845S; MBL is a member of the project consortium
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "Engineering of Pseudomonas putida for fast co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate" at FEMS Conference on Microbiology, Belgrade 2022 (1.7.2022).
Barbora Hrnčířová, Barbora Popelářová, and Matúš Pešta presented their talks at 29th Congress of the Czechoslovak Society for Microbiology, Brno 2022 (15.-17.9.)
Barbora Burýšková presented her talk "Constructing a synthetic Pseudomonas putida consortium for utilization of waste plant biomass oligosaccharides" at 22nd Interdisciplinary Meeting of Young Life Scientists, Milovy 2022 (15.-18.5.)
Year 2021
PUBLICATIONS:
16) Dvořák P, Alvarez-Carreño C, Ciordia S, Paradela A, de Lorenzo V. An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors. Environmental Microbiology 2021, 23(8):4418-4433. doi: https://doi.org/10.1111/1462-2920.15628
15) Espeso DR, Dvořák P, Aparicio T, de Lorenzo V. An automated DIY framework for experimental evolution of Pseudomonas putida. Microbial Biotechnology 2021, 14(6): 2679–2685. doi: https://doi.org/10.1111/1751-7915.13678
PROJECTS:
2021: Grant Agency of Masaryk University (GAMU), Rector's grant for excellent diploma theses (MUNI/C/1811/2020). Construction of simple synthetic bacterial consortium with the division of labour. Principal investigator Stanislav Juračka, supervisor Pavel Dvořák
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "Upgrading Pseudomonas putida by synthetic biology for biotechnological processing of lignocellulosic substrates" at XXVI. Annual Congress of Czech and Slovak Societies for Biochemistry and Molecular Biology 2021 (31.8.2021).
Pavel Dvořák presented a talk entitled "Engineering Pseudomonas putida whole-cell biocatalysts for biotechnological processing of lignocellulosic substrates" at BioTech 2020 (16.6.2021, on-line).
Year 2020
PUBLICATIONS:
14) Dvořák P*, Bayer EA, de Lorenzo V. Surface display of designer protein scaffolds on genome-reduced strains of Pseudomonas putida. (*co-corresponding author) ACS Synthetic Biology. 2020, 9(10):2749–64. doi: https://doi.org/10.1021/acssynbio.0c00276
13) Dvořák P*, Kováč J, de Lorenzo V. Biotransformation of D-xylose to D-xylonate coupled to medium-chain-length polyhydroxyalkanoate production in cellobiose-grown Pseudomonas putida EM42. (*corresponding author) Microbial Biotechnology. 2020, 13(4):1273-83. doi: https://doi.org/10.1111/1751-7915.13574
PROJECTS:
2020: Grant Agency of Masaryk University (GAMU), Rector's grant for excellent diploma theses (MUNI/C/1551/2019). Engineering Pseudomonas putida for co-utilization and valorization of glucose with cellobiose. Principal investigator Dalimil Bujdoš, supervisor Pavel Dvořák
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "Expanding the biocatalytic potential of Pseudomonas putida with surface-exposed designer protein scaffolds" at Applied Synthetic Biology in Europe V (2.-4.11.2020, on-line).
Pavel Dvořák presented a talk entitled "Engineering the interior and exterior of Pseudomonas putida for biotechnological processing of lignocellulosic substrates" at European Biotechnology Congress (24.-26.9.2020, on-line).
Year 2019 (MBL was founded)
PUBLICATIONS:
12) Demko M, Chrást L, Dvořák P, Damborský J, Šafránek D. Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms. 2019 Nov;7(11):553. link
PROJECTS:
2019-2021: Czech Science Foundation (GAČR) Junior Project. Orthogonalization of carbohydrate metabolism in bacterial chassis Pseudomonas putida EM42 for co-utilization of lignocellulose-derived sugars; GJ19-06511Y; principal investigator Pavel Dvořák
2020-2022:Bára Burýšková awarded Brno Ph.D. Talent Fellowship for her project entitled Engineering synthetic bacterial consortia for utilization of plant biomass-derived carbohydrates
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "Empowering Pseudomonas putida with surface-displayed designer protein scaffolds" at FEMS Congress (7.-11.7.2019), Glasgow, UK.
Year 2018
PUBLICATIONS:
11) Dvořák P, de Lorenzo V. Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose. Metabolic Engineering. 2018 Jul 1;48:94–108. link
10) Vanacek P, Sebestova E, Babkova P, Bidmanova S, Daniel L, Dvorak P, et al. Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catalysis. 2018 Mar 2;8(3):2402–12. link
9) Dvorak P, Bednar D, Vanacek P, Balek L, Eiselleova L, Stepankova V, et al. Computer‐assisted engineering of hyperstable fibroblast growth factor 2. Biotechnology and Bioengineering. 2018;115(4):850–62. Article selected for the cover picture of the journal volume in April 2018. link
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "Engineering Pseudomonas putida EM42 for co-utilization of lignocellulose-derived sugars" at Symposium on Biotechnology for Fuels and Chemicals (2.5.2018), Clearwater Beach, Florida, U.S.A.
Year 2017
PUBLICATIONS:
8) Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnology Advances. 2017 Nov 15;35(7):845–66. link
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "Re-factoring Pseudomonas putida for biosynthesis of value-added chemicals from lignocellulosic waste" at EMBO Practical course: Synthetic Biology in Action (27.9.2017), Heidelberg, Germany.
Year 2016
PUBLICATIONS:
7) Brezovsky J, Babkova P, Degtjarik O, Fortova A, Gora A, Iermak I, et al. Engineering a de Novo Transport Tunnel. ACS Catalysis. 2016 Nov 4;6(11):7597–610. link
PROJECTS:
2016-2018: Marie S. Curie Individual Fellowship (H2020-MSCA-IF-2015), project 704410: Re-factoring Pseudomonas putida for biosynthesis of value-added polymers from cellulosic waste (acronym FUTURE), Principal investigator Pavel Dvořák. Project evaluated as a Success Story: https://ec.europa.eu/research/infocentre/article_en.cfm?artid=50765
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "Computer-Assisted Engineering of a Synthetic Biodegradation Pathway: Revisiting Biodegradation with Synthetic Biology" at EUSynBioS Symposium (19.4.2016), Imperial College London, UK.
Year 2015
PUBLICATIONS:
6) Dvorak P, Chrast L, Nikel PI, Fedr R, Soucek K, Sedlackova M, et al. Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway. Microbial Cell Factories. 2015 Dec 21;14(1):201. Among the most influential articles in MCF in 2015 and 2016 based on Altmetric.com. link
Year 2014
PUBLICATIONS:
5) Dvorak P, Kurumbang NP, Bendl J, Brezovsky J, Prokop Z, Damborsky J. Maximizing the Efficiency of Multienzyme Process by Stoichiometry Optimization. ChemBioChem. 2014;15(13):1891–5. link
4) Dvorak P, Bidmanova S, Damborsky J, Prokop Z. Immobilized Synthetic Pathway for Biodegradation of Toxic Recalcitrant Pollutant 1,2,3-Trichloropropane. Environmental Science & Technology. 2014 Jun 17;48(12):6859–66. ACS Editors' Choice (May 24, 2014), best Technology article out of 1,500 papers published in EST in 2014. link
3) Kurumbang NP, Dvorak P, Bendl J, Brezovsky J, Prokop Z, Damborsky J. Computer-Assisted Engineering of the Synthetic Pathway for Biodegradation of a Toxic Persistent Pollutant. ACS Synthetic Biology. 2014 Mar 21;3(3):172–81. link
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "Engineering of Biodegradation Pathway Using Methods of Synthetic Biology" (in Czech) at XXIV. Congress of the Czech and Slovak Societies of Biochemistry and Molecular Biology (18.-21.9.2014) Bratislava, Slovakia and chaired the Biotechnology session of the congress.
Year 2013
PUBLICATIONS:
2) Koudelakova T, Bidmanova S, Dvorak P, Pavelka A, Chaloupkova R, Prokop Z, et al. Haloalkane dehalogenases: biotechnological applications. Biotechnology Journal. 2013;8(1):32–45. link
PROJECTS:
2012-2016: Czech Science Foundation (GAČR). Construction of a Synthetic Metabolic Pathway for Degradation of Important Environmental Pollutant by Protein and Metabolic Engineering; P503/12/0572; principal investigator prof. Jiří Damborský, co-investigator Pavel Dvořák. Project evaluated as excellent.
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "In Vitro and In Silico Engineering of Multi-enzyme Reactions" at Biotrans (21.-25.7.2013) Manchester, UK.
Year 2011
PRESENTATIONS:
Pavel Dvořák presented a talk entitled "In Vitro Protein and Metabolic Engineering of Biodegradation Pathway" at Biotrans (2.-6.10.2011), Giardini Naxos, Italy.
Year 2009
PUBLICATIONS:
1) Klvana M, Pavlova M, Koudelakova T, Chaloupkova R, Dvorak P, Prokop Z, et al. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations. Journal of Molecular Biology. 2009 Oct 9;392(5):1339–56. link
Patents
Dvorak, P., Krejci, P., Balek, L., Eiselleova, L., Konecna, Z., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Stepankova, V., Vanacek, P., Prokop, Z., Damborsky, J., Bosakova, M., 2023: Thermostable FGF2 Polypeptide, Use Thereof. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent US 11,746,135 B2.
Dvorak, P., Krejci, P., Balek, L., Eiselleova, L., Konecna, Z., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Stepankova, V., Vanacek, P., Prokop, Z., Damborsky, J., Bosakova, M., 2022: Thermostable FGF2 Polypeptide, Use Thereof. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent JP7131772.
Dvorak, P., Krejci, P., Balek, L., Eiselleova, L., Konecna, Z., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Stepankova, V., Vanacek, P., Prokop, Z., Damborsky, J., Bosakova, M., 2021: Thermostable FGF2 Polypeptide. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent SG 11201804402W.
Damborsky, J., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Balek, L., Krejci, P., Dvorak, P., Konecna, Z., Eiselleova, L., Bosakova, M., Vanacek, P., Stepankova, V., Prokop, Z., 2020: Thermostable FGF2 Polypeptide, Use thereof and Culture Medium Containing Thermostable FGF2 Polypeptide. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent EP3380508B1.
Dvořák, P., de Lorenzo V., 2019: Recombinant Pseudomonas putida for the production of D-xylonate from D-xylose. Consejo Superior de Investigaciónes Científicas, Spain. Identifier WO2019008131A1.
