Article
Multidisciplinary Sciences
Bo Gao, Liang Liang, Lu Su, Aijia Wen, Chun Zhou, Yu Feng
Summary: Bacterial RecA protein forms filaments with DinI protein in response to DNA damage. These RecA filaments stimulate the autocleavage of LexA, UmuD, and CI, leading to the activation of SOS response and mutagenic repair and lytic cycle. Our study on the structures of RecA filaments in complex with DinI, LexA, UmuD, and CI provides insights into the recognition of conserved protein features in the filament groove, which could be targeted for rational drug design against bacterial SOS response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Olivia P. Duddy, Xiuliang Huang, Justin E. Silpe, Bonnie L. Bassler
Summary: This study highlights the use of quorum sensing for chemical communication between bacteria and phages, specifically in the context of V. cholerae and phage VP882. The research uncovers the molecular mechanisms underlying the asymmetric transcriptional preferences of VqmA proteins, essential for survival and activity of both the pathogen and the phage. The findings shed light on the intricate interplay between bacterial and phage communication systems and their impact on microbial behaviors.
Article
Biology
Anja Pavlin, Anze Lovse, Gregor Bajc, Jan Otonic, Amela Kujovi, Ziva Lengar, Ion Gutierrez-Aguirre, Rok Kostanjsek, Janez Konc, Nadine Fornelos, Matej Butala
Summary: Insights are provided into the action of gp7, a small protein encoded by the bacteriophage GIL01 in the biopesticide Bacillus thuringiensis serovar israelensis. Gp7 hinders the induction of cohabiting prophage pBtic235 and downregulates its genes in a complex with host LexA in stressed cells.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Physical
Prabhat Tripathi, Arash Firouzbakht, Martin Gruebele, Meni Wanunu
Summary: Protein conformational transitions are controlled by chemical kinetics, with passage through an activated state separating different conformational ensembles. The passage time between different states of protein molecules was measured using high-bandwidth nanopore measurements, showing a multidimensional energy landscape for cytochrome c.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Nan Hao, Adrienne E. Sullivan, Keith E. Shearwin, Ian B. Dodd
Summary: The study developed a quantitative in vivo assay for DNA-looping proteins in Escherichia coli, using basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, inserting two binding sites for the candidate looping protein into a pair of operators for the E. coli LacI repressor.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yan Yan, Wenxuan Xu, Sandip Kumar, Alexander Zhang, Fenfei Leng, David Dunlap, Laura Finzi
Summary: Protein-mediated DNA looping is crucial for gene regulation and occurs randomly, with additional proteins increasing the probability. DNA supercoiling, inherent to all genomes, imposes time-constrained emergent behavior on molecular activity.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Asli Azizoglu, Roger Brent, Fabian Rudolf
Summary: The study introduces a new gene expression controller, WTC846, for precise and graded gene expression in Saccharomyces cerevisiae, independent of growth conditions. This controller allows for adjustable protein expression across a range of cellular abundances with limited variation.
Article
Astronomy & Astrophysics
J. Luna Zagorac, Emily Kendall, Nikhil Padmanabhan, Richard Easther
Summary: Ultralight dark matter (ULDM) is a dark matter candidate with a small particle mass. ULDM halos consist of a solitonic core and an NFW-like skirt. By simulating soliton mergers, we studied the core-halo mass relation and found no universal relationship for ULDM.
Editorial Material
Biochemistry & Molecular Biology
Seungha Hwang, Jin Young Kang
Summary: A study reveals the structure and mechanism of the transcription activator CII in phages.
Article
Mathematics
Yunbo Tian, Chao Xia
Summary: This study focuses on the low-degree solution of the Sylvester matrix equation, proving that it has a low-degree solution under certain conditions after substituting parameter variables and assuming the invertibility of certain matrices.
JOURNAL OF MATHEMATICS
(2021)
Article
Biology
Alexander R. Leydon, Wei Wang, Hardik P. Gala, Sabrina Gilmour, Samuel Juarez-Solis, Mollye L. Zahler, Joseph E. Zemke, Ning Zheng, Jennifer L. Nemhauser
Summary: The plant corepressor TOPLESS (TPL) interacts with Mediator proteins to fully repress transcription, while multimer formation has minimal influence on TPL's repression strength.
Article
Biology
Signe Christensen, Sebastian Raemisch, Ingemar Andre
Summary: Chaperones play a crucial role in cellular quality control by removing misfolded and aggregated proteins. The chaperone DnaK responds to molecular stress by recognizing hydrophobic regions of misfolded proteins. This study found that the level of DnaK response is correlated to protein stability when overexpressing recombinant proteins. Additionally, stable proteins showed variability in protein abundance and DnaK response among cells.
COMMUNICATIONS BIOLOGY
(2022)
Article
Genetics & Heredity
Lei Xu, Baihua Sun, Shuang Liu, Xiaotong Gao, Huajie Zhou, Feng Li, Yansha Li
Summary: With the development of gene editing using CRISPR/Cas9 system, the use of dead Cas9 (dCas9) and single guide RNA (sgRNA) has been able to specifically downregulate target gene expression without genomic alteration. This system, known as CRISPR interference (CRISPRi), can be further improved by fusing synthetic transcriptional repressor domains (TRDs) to dCas9. However, the currently used TRD in plants, SRDX, has incomplete repression. In this study, three more effective TRDs (DLN144, DLS, and MIX) were identified in plants, providing more options for CRISPRi application in plants and shedding new light on the advancement of more robust TRDs in plant.
Article
Immunology
Yeqing Zou, Anxing Ge, Brako Lydia, Chen Huang, Qianying Wang, Yanbo Yu
Summary: This study found that gut fungal dysbiosis occurred in the state of hypertension, and fungal dysbiosis can predict the dysregulation of serum light chains in hypertension patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Astronomy & Astrophysics
Donato Bini, Giampiero Esposito
Summary: This paper proposes a toy model in which the Einstein equations are modified by adding a term proportional to the symmetrized partial contraction of the Ricci tensor with the energy-momentum tensor. The resulting effective energy-momentum tensor consists of three contributions and is suitable for dealing with the dark sector of modern relativistic cosmology. The theory coincides with general relativity in vacuum and provides field equations for various metric solutions.