Article
Biotechnology & Applied Microbiology
Ryosuke Fujiwara, Mariko Nakano, Yuuki Hirata, Chisako Otomo, Daisuke Nonaka, Sakiya Kawada, Hikaru Nakazawa, Mitsuo Umetsu, Tomokazu Shirai, Shuhei Noda, Tsutomu Tanaka, Akihiko Kondo
Summary: Research indicates that the localization of specific proteins in the periplasm of Escherichia coli can promote metabolic changes, particularly in the synthesis of aromatic chemicals. This finding offers valuable insights for the development of bioproduction using E. coli.
METABOLIC ENGINEERING
(2022)
Article
Biology
Annette R. Rowe, Farshid Salimijazi, Leah Trutschel, Joshua Sackett, Oluwakemi Adesina, Isao Anzai, Liat H. Kugelmass, Michael H. Baym, Buz Barstow
Summary: Extracellular electron transfer (EET) enables microbial electron uptake for the synthesis of complex organic molecules, but there are significant gaps in understanding the mechanism and genetics of electron uptake.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chang-Kyu Yoon, Deborah Kang, Min-Kyu Kim, Yeong-Jae Seok
Summary: This study reveals that the transcriptional regulator FruR acts as a transcriptional activator of the fru operon in Vibrio cholerae, contrary to other bacteria. The FruR-F1P complex facilitates RNA polymerase binding to the promoter by changing the DNA structure, regulating the expression of PTSFru and FruK in a completely opposite direction among closely related bacterial families.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Puhua Niu, Maria J. Soto, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
Summary: Extensive research has been done on predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes, and for more accurate predictions, both metabolic reactions and genetic regulatory relationships should be modeled. TRIMER is a new modeling and simulation pipeline that integrates transcription regulation with metabolic regulation, demonstrating applicability to both simulated and experimental data.
Article
Biotechnology & Applied Microbiology
Sophia Tsouka, Meric Ataman, Tuure Hameri, Ljubisa Miskovic, Vassily Hatzimanikatis
Summary: The Network Response Analysis (NRA) is a novel framework for rational genetic strain design that integrates various analysis methods and constraints, providing a sophisticated alternative to traditional Metabolic Control Analysis (MCA) for metabolic engineering optimization. It allows for the incorporation of physiological data and the generation of multiple alternative optimal strategies given user-defined boundaries and objectives.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Hye-Young Lee, Chang-Kyu Yoon, Yong-Joon Cho, Jin-Woo Lee, Kyung-Ah Lee, Won-Jae Lee, Yeong-Jae Seok
Summary: The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) not only catalyzes coupled transport and phosphorylation of carbohydrates, but also regulates various physiological processes in most bacteria. The mannose-specific PTS (PTSMan) is suggested to play an important role in host-bacteria interactions in animal-associated bacteria. In Vibrio cholerae, the transcription level of the PTSMan gene is closely related to biofilm formation and host survival rate. The AraC-type transcriptional regulator ManR activates mannose operon transcription and is responsible for V. cholerae growth and biofilm inhibition in the presence of mannose or fructose.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Biochemistry & Molecular Biology
Anzhi Sheng, Jingyi Yang, Longfei Tang, Lili Niu, Liangfen Cheng, Yujing Zeng, Xu Chen, Juan Zhang, Genxi Li
Summary: In this study, a hydrazone chemistry-mediated CRISPR/Cas12a system was proposed and constructed for the first time. The system takes advantage of hydrazone chemistry to accelerate the activation of the CRISPR/Cas12a system and improve its specificity in distinguishing single-base mismatches. The system was successfully applied to analyze Pseudomonas aeruginosa, demonstrating a wide linear range and low detection limit.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Kun-Qiang Hong, Jing Zhang, Biao Jin, Tao Chen, Zhi-Wen Wang
Summary: Synthetic glycine-OFF and -ON riboswitches were successfully designed and screened, showing broad application in tunable regulation, dynamic regulation, and directed evolution of enzymes in E. coli.
MICROBIAL CELL FACTORIES
(2022)
Article
Biochemistry & Molecular Biology
Chang-Kyu Yoon, Seung-Hwan Lee, Jing Zhang, Hye-Young Lee, Min-Kyu Kim, Yeong-Jae Seok
Summary: The phosphorylation state of components of the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) and their interactions with transcription factors play a crucial role in carbon catabolite repression (CCR) by glucose in bacteria. In Vibrio cholerae, the fructose-dependent regulator FruR acts as an activator of the fru operon, contrary to Escherichia coli. The presence of glucose leads to the binding of dephosphorylated HPr to FruR, preventing the FruR-fructose 1-phosphate (F1P) complex from facilitating RNA polymerase (RNAP) binding to the fru promoter.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Julia Ittensohn, Jacqueline Hemberger, Hannah Griffiths, Maren Keller, Simone Albrecht, Thomas Miethke
Summary: The study demonstrates that the uropathogenic Escherichia coli strain CFT073 causes kidney abscesses in mice through the TcpC gene, which is present in around 40% of E. coli isolates of pyelonephritis patients. TcpC impairs host immune response by affecting the TLR signaling chain and NLRP3 inflammasome.
Article
Multidisciplinary Sciences
Ryan T. Santilli, John E. Williamson, Yoshitaka Shibata, Rosalie P. Sowers, Andrew N. Fleischman, Song Tan
Summary: The Penn State Protein Ladder system produces protein molecular weight markers through plasmid expression in E. coli, allowing for easy migration, purification, and detection on SDS-PAGE gels. Additionally, polycistronic expression vectors have been designed for more efficient production and as positive controls for recombinant protein expression and purification in research laboratories.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Prathitha Kar, Sriram Tiruvadi-Krishnan, Jaana Mannik, Jaan Mannik, Ariel Amir
Summary: How cells regulate their cell cycles is a central question for cell biology. This paper presents a study on cell size regulation in Escherichia coli, using conditional independence tests and data on cell size at key cell cycle events. The results suggest that the division event is controlled by the onset of constriction at midcell, and that replication-related processes and additional cues beyond DNA replication play roles in this control.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Medical Laboratory Technology
Jennifer Haynes, Balasubramanian Palaniappan, Eliane Tsopmegha, Uma Sundaram
Summary: Recent studies have shown that human intestinal organoid-derived monolayer cultures can physiologically regulate the apical nutrient and electrolyte transporter function in intestinal cells, similar to observations in in vivo and in vitro animal models. Therefore, this culture model is of great importance for a better understanding of intestinal nutrient absorption regulation.
TRANSLATIONAL RESEARCH
(2022)
Article
Microbiology
Qingli Song, Lishan Zhang, Guibin Wang, Huanhuan Song, Shuangziying Zhang, Jindong Yao, Xiangmin Lin
Summary: This study used quantitative proteomics to compare differentially expressed proteins between the delta ahcirA and wild-type strains of Aeromonas hydrophila. Bioinformatics analysis showed that the expression of peptide, histidine, and arginine ATP-binding cassette (ABC) transporter system-related proteins was significantly higher in the delta ahcirA strain. Further experiments revealed that delta ahcirA grew slower than the wild-type strain in nutrient-limited medium supplemented with dipeptide, histidine, and arginine. Far-western blot analysis confirmed that AhCirA can directly bind to histidine/arginine and dipeptide small-molecule substrates. These findings suggest that AhCirA plays a role in amino acid and peptide uptake as a channel-forming porin and interacts with ABC transporters to transport nutrient substances.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Tuan D. Tran, Munira Aman Ali, Davin Lee, Marie-Anne Felix, Robert J. Luallen
Summary: The study reveals the mechanism by which an intracellular bacterium spreads between intestinal epithelial cells of a natural host by forming filaments. This process is regulated by a conserved nutrient-sensing pathway and reduces host lifespan and fecundity.
NATURE COMMUNICATIONS
(2022)