Article
Biochemistry & Molecular Biology
Honglu Liu, Yaping Chen, Siqi Wang, Yujie Liu, Wanwan Zhao, Kaiyue Huo, Hongfu Guo, Weini Xiong, Shufang Wang, Chao Yang, Ruihua Liu
Summary: This study demonstrates the efficient microbial production of mcl-PHA using a genome-streamlined strain as the chassis and adaptive laboratory evolution for xylose and cellobiose utilization. It also proves the feasibility of using xylose as the sole carbon source for mcl-PHA production and achieves the highest yield of mcl-PHA from cellobiose. The engineered strains derived from genome-reduced P. putida strains show great potential for low-cost production of mcl-PHA from xylose and cellobiose-rich substrates.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Biochemical Research Methods
Shawn Kulakowski, Deepanwita Banerjee, Corinne D. Scown, Aindrila Mukhopadhyay
Summary: Microbial bioconversion is an important approach to produce sustainable chemicals and commodities. However, in industrial-scale bioproduction, anaerobic conditions are preferred due to the high cost of oxygen transfer. Anaerobic bioconversion usually has limited substrate utilization, lower product yields, and reduced final product diversity compared to aerobic processes. This study introduces advances in microbial strain engineering, such as redox cofactor engineering, genome-scale metabolic modeling, and functional genomics, to improve bioproduction processes under low oxygen conditions and enable industrial-scale bioproduction systems.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Yinzhuang Zhu, Mingmei Ai, Xiaoqiang Jia
Summary: Through the design and construction of an artificial microbial consortium, this study successfully enhanced the production of mcl-PHA. A xylose-utilizing E. coli and a mcl-PHA-producing P. putida worked synergistically to achieve efficient accumulation of mcl-PHA.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Dalimil Bujdos, Barbora Popelarova, Daniel C. Volke, Pablo I. Nikel, Nikolaus Sonnenschein, Pavel Dvorak
Summary: This study investigates the basis for the co-utilization of sugars in Pseudomonas putida KT2440 bacteria and proposes a novel genetic engineering strategy to enhance the growth and production of valuable compounds from glucose and cellobiose.
METABOLIC ENGINEERING
(2023)
Article
Physics, Fluids & Plasmas
Ion Santra, Urna Basu, Sanjib Sabhapandit
Summary: This study investigates four distinct dynamical regimes of active Brownian motion in two dimensions, characterized by the presence of two timescales set by the rotational diffusion constant and the reversal rate. Analytical computation of position distribution and persistence exponents reveals that in regime II, the position distribution orthogonal to the initial orientation can be described using a scaled variable, showing nontrivial scaling behavior with a special scaling function. The exact first-passage time distribution computation demonstrates the emergence of a persistence exponent of 1 due to direction reversal in this regime.
Article
Multidisciplinary Sciences
Runyu Zhao, Annesha Sengupta, Albern X. X. Tan, Ryan Whelan, Taylor Pinkerton, Javier Menasalvas, Thomas Eng, Aindrila Mukhopadhyay, Young-Shin Jun, Himadri B. Pakrasi, Yinjie J. Tang
Summary: In this study, the challenge of growth interference in multispecies microbial co-cultures was addressed by encapsulating engineered strains in calcium-alginate hydrogel beads. This allowed the cyanobacterial culture to produce high sucrose concentrations, enabling the production of indigoidine and beta-carotene in the heterotroph. The results showed a significant increase in the yields of indigoidine and beta-carotene compared to the traditional co-culture system.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
William R. Henson, Nicholas A. Rorrer, Alex W. Meyers, Caroline B. Hoyt, Heather B. Mayes, Jared J. Anderson, Brenna A. Black, Lahiru Jayakody, Rui Katahira, William E. Michener, Todd A. VanderWall, Davinia Salvachua, Christopher W. Johnson, Gregg T. Beckham
Summary: This study investigates the biological conversion of methyl phenols in biomass pyrolysis wastewater into 2-methyl and 3-methyl muconic acids for use in polymer building blocks and plasticizers. The converted products show potential performance advantages compared to existing materials, such as reduced melting and glass transition temperatures in nylon analogs and lower water permeability in nylon-6,6 analogs. Incorporating the converted acids into plasticizers for poly(vinyl chloride) also results in lower glass transition temperatures compared to traditional phthalic acid-based plasticizers. Overall, this research highlights the potential for biological waste stream valorization and showcases the advantages of using bio-derived products in various applications.
Article
Chemistry, Multidisciplinary
Hyun Gyu Lim, Thomas Eng, Deepanwita Banerjee, Geovanni Alarcon, Andrew K. Lau, Mee-Rye Park, Blake A. Simmons, Bernhard O. Palsson, Steven W. Singer, Aindrila Mukhopadhyay, Adam M. Feist
Summary: The study utilized Adaptive Laboratory Evolution (ALE) to optimize engineered Pseudomonas putida KT2440 strains with heterologous gene expression for improved utilization of xylose and galactose. Through whole-genome sequencing, transcriptomic analysis, and growth screens, key genes were identified to play significant roles in xylose and galactose growth conditions. The evolved strains successfully produced indigoidine from xylose and galactose, showing potential for broad applications in biomass-utilizing bioprocesses.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Shreya Ghosh, Anam Ejaz, Lucas Repeta, Stewart Shuman
Summary: The study identifies Pseudomonas putida MPE as a novel DNA endonuclease capable of sensing and cutting double-stranded DNA, and hydrolyzing the single-stranded DNA backbone in different orientations to generate distinct cleavage products.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Saba Miri, Seyyed Mohammadreza Davoodi, Mohammad Hossein Karimi Darvanjooghi, Satinder Kaur Brar, Tarek Rouissi, Richard Martel
Summary: The study investigated the co-metabolic biodegradation of p-xylene by Pseudomonas putida in the presence of Benzene, Toluene, and Ethylbenzene. The GMDH model was proposed to predict the transformation of non-growth substrates in the presence of multiple growth substrates, showing potential for accurately predicting the degradation process in co-metabolic systems.
PROCESS BIOCHEMISTRY
(2021)
Article
Microbiology
Justine Turlin, Oscar Puiggene, Stefano Donati, Nicolas T. Wirth, Pablo I. Nikel
Summary: This study investigated the genetic and molecular basis of C1 metabolism in Pseudomonas putida using a systems-level approach. The results identified oxidoreductases encoded by PP_0256 and PP_4596 that were transcriptionally active in the presence of formate and played an important role in C1 tolerance. The study also revealed the detoxification process for methanol and formaldehyde in P. putida. Overall, this research expands our understanding of microbial metabolism and provides a foundation for engineering C1 biomanufacturing.
Article
Biotechnology & Applied Microbiology
Lennart Schada von Borzyskowski, Helena Schulz-Mirbach, Mauricio Troncoso Castellanos, Francesca Severi, Paul A. Gomez-Coronado, Nicole Paczia, Timo Glatter, Arren Bar-Even, Steffen N. Lindner, Tobias J. Erb
Summary: Ethylene glycol (EG) is a promising feedstock for bioprocesses and can be used to produce PET and other polyester fibers and plastics. Currently, most bacteria assimilate EG via the glycerate pathway, which is energy-inefficient and produces CO2. However, the recently discovered BHAC offers a more efficient and carbon-conserving route for EG assimilation.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Hemanoel Passarelli-Araujo, Sarah H. Jacobs, Gloria R. Franco, Thiago M. Venancio
Summary: P. alloputida was proposed as a new species and its population structure includes at least 7 clonal complexes. Clinical isolates are mainly found in one of the complexes, and horizontal gene transfer plays an important role in shaping its ability to bioremediate aromatic compounds.
Article
Biotechnology & Applied Microbiology
Cholpisit Kiattisewee, Chen Dong, Jason Fontana, Widianti Sugianto, Pamela Peralta-Yahya, James M. Carothers, Jesse G. Zalatan
Summary: This study successfully transferred the CRISPRa system to P. putida by optimizing the expression levels of CRISPRa system components and applying rules based on systematic characterization of promoter features, enabling regulation of biosynthesis in the biopterin and mevalonate pathways. Multiple genes can be activated simultaneously by targeting multiple promoters or a single promoter in a multi-gene operon, paving the way for new metabolic engineering strategies in P. putida and other bacterial species.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Christopher Dartiailh, Warren Blunt, Parveen K. Sharma, Song Liu, Nazim Cicek, David B. Levin
Summary: The study found that monomer composition and molecular weight of mcl-PHAs are influenced by substrate choice but do not affect the thermal properties of the material; polymers with the highest molecular weight come from medium chain-length fatty acids, exhibiting the highest crystallinity and tensile strength; while polymers produced from unsaturated, long-chain fatty acids remain amorphous.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Physical
Jan Brezovsky, Petra Babkova, Oksana Degtjarik, Andrea Fortova, Artur Gora, Iuliia Iermak, Pavlina Rezacova, Pavel Dvorak, Ivana Kuta Smatanova, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky
Article
Biotechnology & Applied Microbiology
Pavel Dvorak, David Bednar, Pavel Vanacek, Lukas Balek, Livia Eiselleova, Veronika Stepankova, Eva Sebestova, Michaela Kunova Bosakova, Zaneta Konecna, Stanislav Mazurenko, Antonin Kunka, Tereza Vanova, Karolina Zoufalova, Radka Chaloupkova, Jan Brezovsky, Pavel Krejci, Zbynek Prokop, Petr Dvorak, Jiri Damborsky
BIOTECHNOLOGY AND BIOENGINEERING
(2018)
Article
Chemistry, Physical
Pavel Vanacek, Eva Sebestova, Petra Babkova, Sarka Bidmanova, Lukas Daniel, Pavel Dvorak, Veronika Stepankova, Radka Chaloupkova, Jan Brezovsky, Zbynek Prokop, Jiri Damborsky
Article
Microbiology
Martin Demko, Lukas Chrast, Pavel Dvorak, Jiri Damborsky, David Safranek
Article
Biotechnology & Applied Microbiology
Pavel Dvorak, Jozef Kovac, Victor de Lorenzo
MICROBIAL BIOTECHNOLOGY
(2020)
Article
Biochemical Research Methods
Pavel Dvorak, Edward A. Bayer, Victor de Lorenzo
ACS SYNTHETIC BIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
David R. Espeso, Pavel Dvorak, Tomas Aparicio, Victor deLorenzo
Summary: The study utilized the strategy of Adaptive Laboratory Evolution (ALE) to implement a flexible and automated framework for long-term cultivation experiments on the environmental bacterium Pseudomonas putida. Through analyzing genomic changes, the study revealed the importance of RNA polymerase in controlling overall physiological conditions during the metabolism of a new carbon source.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Microbiology
Pavel Dvorak, Carlos Alvarez-Carreno, Sergio Ciordia, Alberto Paradela, Victor de Lorenzo
Summary: The study reconstructed the structural model of the aromatic binding A domain of XylR in Pseudomonas putida mt-2, providing insights into the mutations affecting effector specificity and the interaction mechanism with aromatic ligands.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Stanislav Obruca, Pavel Dvorak, Petr Sedlacek, Martin Koller, Karel Sedlar, Iva Pernicova, David Safranek
Summary: This review summarizes the current knowledge on PHA accumulation in halophiles and thermophiles, highlighting the advantages of utilizing extremophiles for PHA production. It also discusses recent advances and future perspectives in metabolic engineering and synthetic biology for improving PHA production. The findings and ideas presented in this review suggest that biotechnological production of PHA by extremophiles can be sustainable and economically feasible, enabling PHA to compete with non-biodegradable petrochemical polymers in the market.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Microbiology
Pavel Dvorak, Teca Calcagno Galvao, Katharina Pflueger-Grau, Alice M. Banks, Victor de Lorenzo, Jose I. Jimenez
Summary: The biodegradative capacity of bacteria is influenced by water availability. The activity and specificity of the transcriptional regulator XylR in the biodegradation of m-xylene were examined when water potential was manipulated. Water limitation led to increased effector specificity, which could be counteracted by external addition of glycine betaine. XylR variants were unaffected by water potential and the conformational changes in the A domain and effector-binding pocket were suggested by AlphaFold prediction.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Dalimil Bujdos, Barbora Popelarova, Daniel C. Volke, Pablo I. Nikel, Nikolaus Sonnenschein, Pavel Dvorak
Summary: This study investigates the basis for the co-utilization of sugars in Pseudomonas putida KT2440 bacteria and proposes a novel genetic engineering strategy to enhance the growth and production of valuable compounds from glucose and cellobiose.
METABOLIC ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Esteban Martinez-Garcia, Sofia Fraile, Elena Algar, Tomas Aparicio, Elena Velazquez, Belen Calles, Huseyin Tas, Blas Blazquez, Bruno Martin, Clara Prieto, Lucas Sanchez-Sampedro, Morten H. H. Norholm, Daniel C. Volke, Nicolas T. Wirth, Pavel Dvorak, Lorea Alejaldre, Lewis Grozinger, Matthew Crowther, Angel Goni-Moreno, Pablo Nikel, Juan Nogales, Victor de Lorenzo
Summary: The SEVA platform, launched a decade ago, is a database and physical repository for genetic analysis and engineering. The latest update includes more plasmids and expanded features, making it a popular resource for genetic analysis, genome editing, and bioengineering research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jana Musilova, Xenie Kourilova, Kristyna Hermankova, Matej Bezdicek, Anastasiia Ieremenko, Pavel Dvorak, Stanislav Obruca, Karel Sedlar
Summary: This study presents a comprehensive analysis of three non-model thermophilic bacteria with the ability to produce environmentally friendly alternatives to conventional polyesters. By analyzing the genomic and phenotypic characteristics, the researchers gained valuable insights into the biosynthesis of these alternatives and proposed a comprehensive scheme of carbohydrate metabolism. The study also confirmed the synonymity between Caldimonas and Schlegelella genera.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biotechnology & Applied Microbiology
Pavel Dvorak, Pablo I. Nikel, Jiri Damborsky, Victor de Lorenzo
BIOTECHNOLOGY ADVANCES
(2017)
Article
Biotechnology & Applied Microbiology
Nicolas Huber, Edgar Alberto Alcala-Orozco, Thomas Rexer, Udo Reichl, Steffen Klamt
Summary: Cell-free production systems are commonly used for synthesizing industrial chemicals and biopharmaceuticals. This study presents a model-based optimization framework for cell-free enzyme cascades, taking into account parameter uncertainties. The approach was exemplified using the synthesis of GDP-fucose, resulting in significant improvements in the process.
METABOLIC ENGINEERING
(2024)