Article
Biochemistry & Molecular Biology
Marge Puhm, Johanna Hendrikson, Maia Kivisaar, Riho Teras
Summary: The biofilm of Pseudomonas putida is regulated by various factors, including the cell surface adhesin LapA. Peptides in the growth media have been found to enhance biofilm formation, especially in strains with increased LapA expression. This study investigates the relationship between LapA and peptide-dependent biofilm. It is shown that the vWFa domain in LapA is necessary for the enhancement of biofilm formation by extracellular peptides.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Hyun Gyu Lim, Kevin Rychel, Anand Sastry, Gayle J. Bentley, Joshua Mueller, Heidi S. Schindel, Peter E. Larsen, Philip D. Laible, Adam M. Guss, Wei Niu, Christopher W. Johnson, Gregg T. Beckham, Adam M. Feist, Bernhard O. Palsson
Summary: This study applies a machine-learning approach to uncover the genome-scale transcriptional regulatory network in Pseudomonas putida KT2440, providing a basis for understanding its physiological processes and engineering it for practical use.
METABOLIC ENGINEERING
(2022)
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
Microbiology
Marge Puhm, Hanna Ainelo, Maia Kivisaar, Riho Teras
Summary: Extracellular factors and growth conditions can influence the formation and development of bacterial biofilms. The components of the medium play an important role in the biofilm development of Pseudomonas putida. Tryptone in the LB medium is found to maintain the biofilm in its older stages. Other biopolymers have variable effects on biofilm formation, indicating the influence of multiple bacterial factors.
Article
Environmental Sciences
Kaiyue Huo, Siqi Wang, Wanwan Zhao, Hongfu Guo, Weini Xiong, Ruihua Liu, Chao Yang
Summary: In this study, the first engineered DCA-mineralizing strain KTU-P8DCA was constructed by enhancing pathway expression with a strong promoter P8 in the biosafety strain Pseudomonas putida KT2440. Strain KTU-P8DCA exhibited superior tolerance to high concentrations of DCA and showed excellent genetic stability in continuous passage culture. This research has significant implications for the bioremediation of sites heavily contaminated with DCA.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biology
Jinjin Diao, Rhiannon Carr, Tae Seok Moon
Summary: In this study, we identified and studied the transcription factors involved in aromatic degradation in Rhodococcus opacus using GFP-based sensors and comprehensive deletion analyses. Our results indicate that the funneling pathways for different aromatic compounds are regulated by transcriptional activators or repressors. Additionally, the substrate hierarchy in R. opacus may be due to the transcriptional cross-regulation of different aromatic funneling pathways.
COMMUNICATIONS BIOLOGY
(2022)
Article
Engineering, Environmental
Kaiyue Huo, Yujie Liu, Rui Huang, Yiting Zhang, Honglu Liu, You Che, Chao Yang
Summary: A novel promoter engineering-based strategy was developed to create efficient PNP-mineralizing bacteria by introducing a complete PNP biodegradation pathway from Pseudomonas sp. strain WBC-3 into the genome of a biosafety and soil-dwelling bacterium Pseudomonas putida KT2440. Five strong promoters were identified from P. putida KT2440 and independently inserted into the genome to create a mutant strain with the highest PNP degradation rate and strong tolerance against high concentrations of PNP, demonstrating complete and efficient PNP mineralization. This strategy opens new avenues for creating efficient degraders for bioremediation.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Cell Biology
Kunie Yoshinaga-Sakurai, Toby G. Rossman, Barry P. Rosen
Summary: AS3MT is a human enzyme that catalyzes arsenic biotransformations and is considered to contribute to arsenic-related diseases. The expression of AS3MT is tissue/cell type-specific, and the transcriptional regulation mechanism of the gene is still unknown. In this study, the core promoter region of the human AS3MT gene is defined, and a GC box in the promoter is identified as a site where the transcription factor Sp1 binds, indicating the involvement of regulatory elements in AS3MT gene expression.
CELL BIOLOGY AND TOXICOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yiting Zhang, Honglu Liu, Yujie Liu, Kaiyue Huo, Shufang Wang, Ruihua Liu, Chao Yang
Summary: This study successfully increased the PHA yield by screening endogenous strong promoters from P. putida KT2440, demonstrating the potential of this strategy for enhanced production of secondary metabolites and heterologous proteins in P. putida KT2440.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Honglu Liu, Yaping Chen, Yiting Zhang, Wanwan Zhao, Hongfu Guo, Siqi Wang, Wenjie Xia, Shufang Wang, Ruihua Liu, Chao Yang
Summary: A novel strategy of genome streamlining combined with promoter engineering was developed in P. putida KT2440 for constructing the minimal genome cell factories (MGF) capable of efficiently producing medium-chain-length PHA (mcl-PHA). The highest PHA yield with P. putida KT2440 was obtained with the optimized genome strain KTU-U27Agcd-P46CA, suggesting the feasibility of genome streamlining in synthetic biology applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Multidisciplinary Sciences
I. Cody MacDonald, Travis R. Seamons, Jonathan C. Emmons, Shwan B. Javdan, Tara L. Deans
Summary: Expansion of genetic toolkits for prokaryotic synthetic biology can enhance gene expression dynamics. Integrating the eukaryotic transcription factor QF into E. coli allows for the construction of genetic devices with complex functions.
NATURE COMMUNICATIONS
(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
Biochemistry & Molecular Biology
Eduardo Lujan-Soto, Paola Aguirre de la Cruz, Vasti T. Juarez-Gonzalez, Jose L. Reyes, Maria de la Paz Sanchez, Tzvetanka D. Dinkova
Summary: In recent years, miR528 has been found to play important roles in plant development and stress response. This study examined the transcription regulation and molecular mechanisms of MIR528 expression in maize, revealing conserved transcription factor binding sites and demonstrating the up-regulation of miR528 expression by exogenous nitrate and auxin treatments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Sara S. Procknow, Beth A. Kozel
Summary: Elastin provides elasticity to tissues such as the lung, blood vessels, and skin, but the mechanisms regulating its production are not fully understood. Studying the expression of the ELN gene may help intervene in rare diseases and potentially replace age-related losses by re-initiating elastin production.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Xuejiao Huang, Daihua Jiang, Jiupai Ni, Deti Xie, Zhenlun Li
Summary: The bacterium Pseudomonas putida Y-9 efficiently removes ammonium and nitrate through assimilation, with almost no harmful nitrite accumulation.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2021)
Article
Multidisciplinary Sciences
Andrio Lahesaare, Hanna Ainelo, Annika Teppo, Maia Kivisaar, Hermann J. Heipieper, Riho Teras
Article
Microbiology
Julia Jakovleva, Annika Teppo, Anna Velts, Signe Saumaa, Hanna Moor, Maia Kivisaar, Riho Teras
Article
Microbiology
Hanna Moor, Annika Teppo, Andrio Lahesaare, Maia Kivisaar, Riho Teras
Article
Multidisciplinary Sciences
Andrio Lahesaare, Hanna Moor, Maia Kivisaar, Riho Teras
Article
Multidisciplinary Sciences
Annika Teppo, Andrio Lahesaare, Hanna Ainelo, Kadri Samuel, Maia Kivisaar, Riho Teras
Article
Microbiology
Marge Puhm, Hanna Ainelo, Maia Kivisaar, Riho Teras
Summary: Extracellular factors and growth conditions can influence the formation and development of bacterial biofilms. The components of the medium play an important role in the biofilm development of Pseudomonas putida. Tryptone in the LB medium is found to maintain the biofilm in its older stages. Other biopolymers have variable effects on biofilm formation, indicating the influence of multiple bacterial factors.
Article
Biochemistry & Molecular Biology
Hedvig Tamman, Karin Ernits, Mohammad Roghanian, Andres Ainelo, Christina Julius, Anthony Perrier, Ariel Talavera, Hanna Ainelo, Remy Dugauquier, Safia Zedek, Aurelien Thureau, Javier Perez, Gipsi Lima-Mendez, Regis Hallez, Gemma C. Atkinson, Vasili Hauryliuk, Abel Garcia-Pino
Summary: Stringent factors regulate bacterial cell reprogramming by increasing the level of (p)ppGpp. This study presents the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and reveals the intramolecular regulation mechanism of 'long'-stringent factors. The Core subdomain plays a key role in determining the specialization of long RelA-SpoT homologs towards synthesis or hydrolysis.
NATURE CHEMICAL BIOLOGY
(2023)
