Article
Chemistry, Multidisciplinary
Shrilaxmi Bhat, Anantika Banerjee, Swathi Alagesan
Summary: In this study, a synthetic biosensor based on the AraC-pBAD system was designed and constructed, with the ligand-binding domain of AraC replaced by IsoA. Fluorescence output was observed only when wild-type Escherichia coli cells were induced with both isoprene and arabinose. The biosensor sensitivity and dynamic range were enhanced by removing operator sequences and by using a strong tac promoter. This study provides a prototype for developing chimeric AraC-based biosensors and opens new avenues for further study and exploration.
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
Chemistry, Multidisciplinary
Charles Burridge, Christopher A. Waudby, Tomasz Wlodarski, Anais M. E. Cassaignau, Lisa D. Cabrita, John Christodoulou
Summary: This study used solution-state NMR spectroscopy to measure transverse proton relaxation rates for methyl groups in folded ribosome-nascent chain complexes, revealing interactions between the nascent chain and ribosome surface driven predominantly by electrostatics. By observing changes in these interactions as subsequent domain emerges, the impact on free energy landscapes associated with co-translational folding process can be deduced.
Article
Multidisciplinary Sciences
Negin Malekian, Amay A. Agrawal, Thomas U. Berendonk, Ali Al-Fatlawi, Michael Schroeder
Summary: This study investigates the positively selected genes in wastewater E. coli and finds that some of them are functionally associated with antibiotic resistance. Mutations associated with antibiotic resistance are also identified. The findings provide novel insights into the mechanisms driving antibiotic resistance.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Jack M. Moen, Kyle Mohler, Svetlana Rogulina, Xiaojian Shi, Hongying Shen, Jesse Rinehart
Summary: Protein phosphorylation is a crucial post-translational modification that regulates cellular processes and protein-protein interactions. Traditional strategies for functional assignment of phosphorylation events have become inadequate in keeping up with the rapid identification pace through proteomic surveillance. However, the development of phospho-amino-acid-specific orthogonal translation systems offers a kinase-independent method to assess the physiological function of phosphorylation.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
James A. Martin, Arthur G. Palmer
Summary: This study reveals the kinetic model of the handle region in the ribonuclease HI homologs, including transitions between different conformations. The research findings show that the homologs containing asparagine 88 have distinct structural features compared to those containing arginine or lysine 88.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Cell Biology
Meihui Cui, Tao Sun, Shubin Li, Huizhuo Pan, Jing Liu, Xinyu Zhang, Lianyue Li, Shanshan Li, Chunyang Wei, Chengzhuang Yu, Chun Yang, Ning Ma, Binglin Ma, Shenjunjie Lu, Jin Chang, Weiwen Zhang, Hanjie Wang
Summary: Recombinant bacterial colonization is essential in disease prevention, alleviation, and treatment, with the success of application hinges on efficient spatiotemporal colonization of host gut. The use of engineered upconversion microgels and light-responsive bacteria in this study demonstrated controlled and effective colonization of EcN, which successfully alleviated DSS-induced colitis in mice, potentially advancing the clinical application of engineered microbial therapeutics.
Article
Biochemistry & Molecular Biology
Kumari Kavita, Aixia Zhang, Chin-Hsien Tai, Nadim Majdalani, Gisela Storz, Susan Gottesman
Summary: Hfq, a bacterial RNA chaperone, plays a crucial role in stabilizing small regulatory RNAs and facilitating their interactions with target mRNAs. Deletion of the C-terminal domain in Hfq leads to defects in the accumulation and function of various sRNAs, particularly those that bind to the distal face. The region between amino acids 66-72 is essential for this defect, while the CTD region beyond amino acid 72 is important for functions associated with the Hfq rim.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Pietro Ridone, Tsubasa Ishida, Angela Lin, David T. Humphreys, Eleni Giannoulatou, Yoshiyuki Sowa, Matthew A. B. Baker
Summary: This study used CRISPR engineering to replace the stator genes in the bacterial motor and analyzed the genes related to bacterial adaptation through whole-genome and RNA sequencing. The results showed that the stator has the ability to spontaneously revert in a low-sodium environment, highlighting the hierarchical modularity of the motor.
Article
Ecology
Alejandra Rodriguez-Verdugo, Martin Ackermann
Summary: The study showed that in a constant commensal environment, two species can coexist, but in a fluctuating environment, one species is likely to go extinct, which was highly deterministic. This extinction was driven by adaptive mutations in a small set of genes.
Article
Biochemistry & Molecular Biology
Joanne M. L. Ho, Corwin A. Miller, Sydney E. Parks, Jacob R. Mattia, Matthew R. Bennett
Summary: This study introduces a leak dampener tool that reduces leak in inducible genetic systems, demonstrated with two biosensors. The tool, based on a feedforward loop, shows promise for improving gene expression control in synthetic biology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Xiao Yi, Joleen Khey, Romas J. Kazlauskas, Michael Travisano
Summary: In order to explore the sequence space of proteins extensively, in vivo evolution with large populations is required. A targeted artificial DNA replisome (TADR) protein complex was designed to replicate a plasmid with errors in live cells, enhancing mutation rates of the target plasmid significantly while minimizing off-target mutagenesis. Evolving itself to increase error rates and improve the efficiency of an efflux pump, TADR enables multiple simultaneous substitutions to discover new functions in molecular evolution.
Article
Veterinary Sciences
Nicola Palmieri, Ilias Apostolakos, Surya Paudel, Michael Hess
Summary: This study identified gene variations and SNPs associated with APEC pathogenicity, suggesting the involvement of multiple regulated pathways. The findings also suggest the importance of nutrient uptake and defense from the host immune system in APEC pathogenicity.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Multidisciplinary Sciences
Philipp Wendering, Marius Arend, Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: Turnover numbers of enzymes are a key property that can improve the prediction accuracy of cellular phenotypes in metabolic modeling. However, in vitro and in vivo turnover numbers alone do not lead to accurate predictions of condition-specific growth rates of E. coli and S. cerevisiae, especially when considering protein abundances. By correcting turnover numbers using proteomics and physiological data, we demonstrate improved predictions of condition-specific growth rates. Our approach provides a means to correct turnover numbers and catalog kcatomes of other organisms.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Francois Bertaux, Sebastian Sosa-Carrillo, Viktoriia Gross, Achille Fraisse, Chetan Aditya, Mariela Furstenheim, Gregory Batt
Summary: Small-scale, low-cost bioreactors are gaining popularity in quantitative systems and synthetic biology. In this study, the authors present ReacSight, a strategy that enhances bioreactor arrays by connecting them with sensitive measurement devices using low-cost pipetting robots. They demonstrate the capabilities of ReacSight in yeast, including real-time optogenetic control of gene expression, exploration of nutrient scarcity effects on fitness and cellular stress, and dynamic control of a two-strain consortium's composition.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Fabiana Malaga, Ory Mayberry, David J. Park, Michael E. Rodgers, Dmitri Toptygin, Robert F. Schleif
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2016)
Article
Genetics & Heredity
S. Amer Riazuddin, David S. Parker, Elyse J. McGlumphy, Edwin C. Oh, Benjamin W. Iliff, Thore Schmedt, Ula Jurkunas, Robert Schleif, Nicholas Katsanis, John D. Gottsch
AMERICAN JOURNAL OF HUMAN GENETICS
(2012)
Article
Biochemistry & Molecular Biology
Michael E. Rodgers, Robert Schleif
Article
Biochemistry & Molecular Biology
Robert F. Schleif
Article
Microbiology
Jennifer Seedorff, Robert Schleif
JOURNAL OF BACTERIOLOGY
(2011)
Article
Biochemistry & Molecular Biology
Katherine E. Frato, Robert F. Schleif
JOURNAL OF MOLECULAR BIOLOGY
(2009)
Article
Biochemistry & Molecular Biology
Monica Berrondo, Jeffrey J. Gray, Robert Schleif
JOURNAL OF MOLECULAR BIOLOGY
(2010)
Article
Biochemistry & Molecular Biology
Jennifer E. Seedorff, Michael E. Rodgers, Robert Schleif
Article
Biochemistry & Molecular Biology
Ana Damjanovic, Benjamin T. Miller, Robert Schleif
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2013)
Article
Biochemistry & Molecular Biology
Stephanie Dirla Cole, Robert Schleif
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2012)
Article
Biochemistry & Molecular Biology
Mary Lowe, David Gullotti, Ana Damjanovic, Ann Cheng, Stephanie Dirla, Robert Schleif
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2014)
Article
Biochemistry & Molecular Biology
Alexander Tischer, Matthew J. Brown, Robert F. Schleif, Matthew Auton
Article
Biochemistry & Molecular Biology
Matthew J. Brown, Robert Schleif
Review
Microbiology
Robert Schleif
FEMS MICROBIOLOGY REVIEWS
(2010)