Article
Biochemistry & Molecular Biology
Yixuan Cui, Ying Jiang, Meng Xiao, Muhammad Zeeshan Munir, Sadaf Riaz, Faiz Rasul, Maurycy Daroch
Summary: Ethylene, an important chemical, can be produced through a cleaner method, reducing environmental pollution. By evaluating the catalytic activity of different protein sequences, this study demonstrated their ability to generate ethylene.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Lea Vidal, Esteban Lebrun, Young-Kyoung Park, Guillaume Mottet, Jean-Marc Nicaud
Summary: In this study, novel bidirectional and hybrid bidirectional promoters were developed, whose expression can be fine-tuned to meet the demand for versatile promoters in the yeast Y. lipolytica. This study provides effective tools for smoothly adjusting the erythritol-inducible co-expression of two target genes in biotechnology applications. BDPs developed in this study have potential applications in the fields of heterologous protein production, metabolic engineering, and synthetic biology.
MICROBIAL CELL FACTORIES
(2023)
Article
Microbiology
Jai Kumar Gupta, Shireesh Srivastava
Summary: The study demonstrates that the choice of photosynthetic promoters and RBS sequences can impact growth and glycogen accumulation in SbtA-overexpressing cells. Specifically, P-cpcB or P-cpcB(560) were more effective than P-rbcL(2), and RBS2 was more effective than RBS1 in increasing growth and glycogen content.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Salva Duran-Nebreda, Jordi Pla, Blai Vidiella, Jordi Pinero, Nuria Conde-Pueyo, Ricard Sole
Summary: This article discusses the characteristics of multicellular entities and their spatial patterns related to functions, as well as the repeating distributions in biological structures. It introduces patterning modules and synthetic gene circuits, along with the phenomenon of symmetry-breaking demonstrated through experimental results.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Sandra Mittermair, Gergely Lakatos, Cecilia Nicoletti, Karolina Ranglova, Joao Camara Manoel, Tomas Grivalsky, Daniyar Malikuly Kozhan, Jiri Masojidek, Juliane Richter
Summary: Low production rates are a limiting factor for industrial climate-neutral production of biovaluable compounds in cyanobacteria. Genes involved in glycogen synthesis pathway were combined with specific promoters and cloning sites to select the most productive transformants, with glgA1_11 and glgC_2 showing significantly increased biomass and glycogen production after 96 hours, making them promising energy sources for further applications.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Carolyn N. Bayer, Maja Rennig, Anja K. Ehrmann, Morten H. H. Norholm
Summary: The article introduces a simple genome engineering method called SEGA, which combines DNA and bacterial cells for synthesis, and then identifies recombinant clones through color change occurring on agar plates. The modular nature of SEGA allows for standardization of genetic designs and broad application range to be achieved.
NATURE COMMUNICATIONS
(2021)
Review
Biology
Xiaofan Feng, Mario Andrea Marchisio
Summary: Promoters are DNA sequences that play a crucial role in initiating transcription. They can function constitutively or be regulated by different environmental signals. The strength of promoters significantly impacts the expression of proteins and RNA in yeast genetic circuits. Advances in promoter engineering have been driven by Synthetic Biology, with a focus on constructing artificial promoters for genetic circuits in popular chassis like S. cerevisiae.
Review
Microbiology
Barbara Bourgade, Karin Stensjo
Summary: Genetic engineering and synthetic biology in marine cyanobacteria have great potential for a greener future, although further research is needed. Comparisons with freshwater cyanobacteria can provide guidance for the application of marine species.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Luna Rizik, Loai Danial, Mouna Habib, Ron Weiss, Ramez Daniel
Summary: Researchers have utilized the perceptgene technology to create synthetic gene circuits based on the computational properties of neuronal networks. These circuits can perform non-binary logic computation and signal processing, and can be modified for different tasks by adjusting parameters.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Jiliang Deng, Yanling Wu, Zhaohui Zheng, Nanzhu Chen, Xiaozhou Luo, Hongting Tang, Jay D. Keasling
Summary: In this study, a library of synthetic GAL promoters was constructed, demonstrating a synergistic relationship between upstream activating sequences (UASs) and core promoters in determining promoter performance under different carbon sources. By manipulating UAS sequence, number, and substitution, the strength of synthetic GAL promoters could be fine-tuned. Core promoter replacement resulted in synthetic promoters with a twofold improvement in strength compared to the classic GAL1 promoter under multiple carbon sources in a strain with GAL1 and GAL80 engineering, expanding the dynamic range and carbon source tolerance of the GAL expression system.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemical Research Methods
Chandra Kanth Bandi, Kyle S. Skalenko, Ayushi Agrawal, Neelan Sivaneri, Margaux Thiry, Shishir P. S. Chundawat
Summary: The study developed an engineered synthetic promoter system called cyn regulon to selectively detect azide ions and induce downstream expression of reporter genes. The engineered cyn azide operon showed highly tunable expression over a range of azide ion concentrations and rapidly induced reporter gene expression.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Engineering, Biomedical
Isabella M. Goodchild-Michelman, George M. Church, Max G. Schubert, Tzu-Chieh Tang
Summary: Cyanobacteria are promising for developing carbon neutral and carbon negative technologies due to their efficient photosynthesis and easy genetic manipulation. Although researchers have demonstrated their ability to produce sustainable biomaterials, industrial application is still in its early stages.
MATERIALS TODAY BIO
(2023)
Article
Biochemical Research Methods
Dairio Neves, Ulf W. Liebal, Salome C. Nies, Tobias B. Alter, Christian Pitzler, Lars M. Blank, Birgitta E. Ebert
Summary: By characterizing libraries of synthetic and sigma;(70)-dependent promoters, researchers compared the expression of promoters in both Escherichia coli TOP10 and Pseudomonas taiwanensis VLB120. They quantitatively described the strength of the promoters, expanded the genetic toolbox of P. taiwanensis VLB120, and evaluated its potential as a chassis for biotechnology applications.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Kristoffer Bach Falkenberg, Vivienne Mol, Arrate Sainz de la Maza Larrea, Ivan Pogrebnyakov, Morten H. H. Norholm, Alex Toftgaard Nielsen, Sheila Ingemann Jensen
Summary: Versatile DNA assembly standards and well-characterized part libraries are crucial tools in synthetic biology. Despite limitations in vector standards for Gram-positive hosts, the ProUSER2.0 toolbox provides a standardized platform for creating shuttle vectors in Bacillus subtilis. This system is semi-compatible with previously developed standards and allows for efficient insertion of cargo sequences. Through thorough characterization of integration sites and promoters, the toolbox facilitates the construction of signal peptide libraries for industrial proteins. Overall, the ProUSER2.0 toolbox is a powerful and flexible framework for use in B. subtilis.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Plant Sciences
Alfonsina Milito, Moritz Aschern, Josie L. McQuillan, Jae-Seong Yang
Summary: This review focuses on Chlamydomonas reinhardtii, a microalgal species commonly used in bioengineering research, and discusses the key obstacles and potential solutions in synthetic promoter development. Microalgae have great potential as carbon-fixing biofactories to provide safe and sustainable high-value compounds, but optimizing their metabolic outputs and making them competitive with established industrial hosts requires precise control over transgene expression. However, the current repertoire of functional synthetic promoters for microalgae, especially for C. reinhardtii, is limited compared to other commercial chassis. The review highlights the need to expand the microalgal gene expression toolbox and proposes novel approaches and perspectives for synthetic promoter development in microalgae.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biotechnology & Applied Microbiology
Rongming Liu, Liya Liang, Alaksh Choudhury, Andrew D. Garst, Carrie A. Eckert, Eun Joong Oh, James Winkler, Ryan T. Gill
METABOLIC ENGINEERING
(2019)
Article
Chemistry, Multidisciplinary
Yuchen Ding, John R. Bertram, Carrie Eckert, Rajesh Reddy Bommareddy, Rajan Patel, Alex Conradie, Samantha Bryan, Prashant Nagpal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Multidisciplinary Sciences
R. M. Liu, L. L. Liang, E. Freed, H. Chang, E. Oh, Z. Y. Liu, A. Garst, C. A. Eckert, R. T. Gill
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Rongming Liu, Liya Liang, Emily F. Freed, Alaksh Choudhury, Carrie A. Eckert, Ryan T. Gill
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Eun Joong Oh, Rongming Liu, Liya Liang, Emily F. Freed, Carrie A. Eckert, Ryan T. Gill
ACS SYNTHETIC BIOLOGY
(2020)
Article
Biochemical Research Methods
Liya Liang, Rongming Liu, Emily F. Freed, Carrie A. Eckert, Ryan T. Gill
Summary: The study targeted the active sites of transcriptional regulators to identify mutants with tolerance to isopropanol and isobutanol, revealing underlying mechanisms for improved stress tolerance and promising strategies for enhancing tolerance to C3-C4 alcohols through perturbation of the transcriptional regulatory network.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biology
Maria Priscila Lacerda, Eun Joong Oh, Carrie Eckert
Article
Biotechnology & Applied Microbiology
Sophie Vaud, Nicole Pearcy, Marko Hanzevacki, Alexander M. W. Van Hagen, Salah Abdelrazig, Laudina Safo, Muhammad Ehsaan, Magdalene Jonczyk, Thomas Millat, Sean Craig, Edward Spence, James Fothergill, Rajesh Reddy Bommareddy, Pierre-Yves Colin, Jamie Twycross, Paul A. Dalby, Nigel P. Minton, Christof M. Jaeger, Dong-Hyun Kim, Jianping Yu, Pin-Ching Maness, Sean Lynch, Carrie A. Eckert, Alex Conradie, Samantha J. Bryan
Summary: Ethylene is a widely used small hydrocarbon gas in the chemical industry, but its production contributes to significant CO2 emissions, highlighting the need for a sustainable alternative. Research has shown that a combination of genome-scale metabolic modeling, continuous fermentation, and protein evolution can accelerate the development of a high-efficiency ethylene-producing E. coli strain, resulting in a 49-fold increase in production.
METABOLIC ENGINEERING
(2021)
Article
Biochemical Research Methods
Monica Prias-Blanco, Timothy M. Chappell, Emily F. Freed, Eudald Illa-Berenguer, Carrie A. Eckert, Wayne A. Parrott
Summary: Auxotrophic strains of Agrobacterium tumefaciens play an important role in the development of efficient transformation systems, especially for crops that are historically difficult to transform. The use of auxotrophic strains reduces bacterial overgrowth and the need for antibiotics.
TRANSGENIC RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Jacob A. Fenster, Allison Z. Werner, Jian Wei Tay, Matthew Gillen, Leo Schirokauer, Nicholas C. Hill, Audrey Watson, Kelsey J. Ramirez, Christopher W. Johnson, Gregg T. Beckham, Jeffrey C. Cameron, Carrie A. Eckert
Summary: This study evaluates the application of an inducible CRISPRi toolset on various targets and finds that it can be tightly regulated when using a dual-inducible promoter. Single cell time lapse microscopy reveals intrinsic heterogeneity in knockdown rate within an isoclonal population and identifies a quiescent phase before a phenotypic response occurs. Using this toolset, researchers successfully produce a monomer for nylon production by knocking down a specific operon.
METABOLIC ENGINEERING COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Gur Pines, Assaf Pines, Carrie A. Eckert
Summary: Saturation mutagenesis is a protein engineering method that involves changing amino acids at specific sites. A codon compression algorithm is used to select degenerate codons, and a web tool is developed to consider the distance between the wild-type codon and the library for library design.
Article
Chemistry, Multidisciplinary
Zhaodong Li, Chao Wu, Xiang Gao, Bennett Addison, Shrameeta Shinde, Xin Wang, Xihan Chen, Jianping Yu, Drazenka Svedruzic, Jeffrey L. Blackburn, Wei Xiong
Summary: A new integrated photo-electrochemical system has been developed, allowing direct electron transfer to the photosynthetic system in living cyanobacteria. This system enables the conversion of CO2 into acetate by fueling cyanobacteria with both illumination and exogenous electrons. The energy conversion efficiency for acetate production under intermittent LED illumination and exogenous electron supply reached around 9%, suggesting potential for sustainable biofuel production.
ENERGY & ENVIRONMENTAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Bo Wang, Yao Xu, Xin Wang, Joshua S. Yuan, Carl H. Johnson, Jamey D. Young, Jianping Yu
Summary: The metabolic pathways used by microbes to degrade or mitigate the toxicity of guanidine remain unclear. This study reveals a guanidine degrading enzyme in cyanobacteria that enhances genomic stability and enables sustained high-level ethylene production, demonstrating biotechnological applications for natural guanidine degradation pathways.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Julie E. Walker, Anthony A. Lanahan, Tianyong Zheng, Camilo Toruno, Lee R. Lynd, Jeffrey C. Cameron, Daniel G. Olson, Carrie A. Eckert
METABOLIC ENGINEERING COMMUNICATIONS
(2020)
Article
Chemistry, Multidisciplinary
Bo Wang, Tao Dong, Aldon Myrlie, Liping Gu, Huilan Zhu, Wei Xiong, PinChing Maness, Ruanbao Zhou, Jianping Yu