Article
Multidisciplinary Sciences
Zhou Yin, Jeremy G. Bird, Jason T. Kaelber, Bryce E. Nickels, Richard H. Ebright
Summary: The article investigates the mechanism of action of Q proteins in transcription in Lambdoid bacteriophage. The results show that Q proteins form a nozzle-like structure to prevent pause and termination of RNA polymerase during transcription. Compared to previous studies, this research reveals the structural and functional differences of Q proteins in different bacteriophages.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Bing Wang, Irina Artsimovitch
Summary: The timely and accurate RNA synthesis is dependent on accessory proteins like NusG/Spt5 that regulate RNA polymerase. NusG family is universally conserved but actively evolving, with specialized regulators like LoaP, RfaH, and UpxY emerging through horizontal gene transfer. Despite having a common origin, NusG homologs have different effects on RNA synthesis, aiding bacterial adaptation to diverse ecological niches.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Freya D. R. Wencker, Gabriella Marincola, Sonja M. K. Schoenfelder, Sandra Maass, Doerte Becher, Wilma Ziebuhr
Summary: In Staphylococcus aureus, de novo methionine biosynthesis is regulated by a unique hierarchical pathway involving stringent-response controlled CodY repression in combination with a T-box riboswitch and RNA decay. The secondary structure of the met leader RNA includes a terminator helix target for RNase III endoribonucleolytic cleavage.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Amr Elghondakly, Chih Hao Wu, Steven Klupt, Jonathan Goodson, Wade C. Winkler
Summary: Bacterial NusG interacts with RNA polymerase through its N-terminal domain, and its C-terminal domain forms dynamic interactions with various factors to affect transcription elongation. LoaP binds to a small RNA hairpin in the 50 leader region of its target operons with high affinity and specificity, expanding the repertoire of macromolecular interactions exhibited by NusG.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jonathan Jagodnik, Brian Tjaden, Wilma Ross, Richard L. Gourse
Summary: Ligand-binding RNAs, known as RNA aptamers, are abundant in all three domains of life and play a role in sensing metabolites and small molecules. This study introduces a method called RNA-DRaCALA, which allows for the rapid screening of numerous RNA aptamers by examining their ligand binding. Using this method, 30 RNA aptamers were screened for their ability to bind (p)ppGpp, and key features distinguishing between ppGpp and pppGpp binding sites were identified. Additionally, the method was shown to be effective in analyzing binding of aptamers with thiamine pyrophosphate.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yinshan Yang, Jerome Gracy, Nathalie Declerck, Helene Demene
Summary: LicT is an antiterminator protein of the BglG family involved in bacterial carbohydrate catabolism control. The unique structure and signal transduction mechanism of LicT play a crucial role in this process. The study demonstrates that specific conformational changes induced by mutations can activate LicT, and the active conformation of the PRD1 regulation domain transmits signals to CAT through a network of negatively charged residues.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Adrian Boicean, Victoria Birlutiu, Cristian Ichim, Olga Brusnic, Danusia Maria Onisor, Amedeo Amedei, Ryota Niikura
Summary: Imbalances in the gut microbiota play a crucial role in the development of liver diseases, and fecal microbiota transplantation has shown promise as an effective treatment for chronic liver diseases and cirrhosis.
Review
Immunology
Solveig Runge, Stephan Patrick Rosshart
Summary: The field of microbiome research has rapidly developed and become a major topic of interest for various research fields and industries. The microbiome, including various microorganisms and their genes, plays a crucial role in mammalian physiology, particularly in immune system development and function. Studies should not only focus on the gut bacterial microbiota, but also consider the impact of other microorganisms on host immunity.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Ecology
Alan Emanuel Silva Cerqueira, Tobin J. Hammer, Nancy A. Moran, Weyder Cristiano Santana, Maria Catarina Megumi Kasuya, Cynthia Canedo da Silva
Summary: A study on Brazilian stingless bees revealed that they lack common bacterial symbionts Snodgrassella and Gilliamella found in other social corbiculate bees, instead harboring more environmental bacteria and bee-specific Starmerella yeasts. This indicates ecological shifts or acquisition of new symbionts as functional replacements in the stingless bees.
Article
Biochemistry & Molecular Biology
Jorge A. Marchand, Merrick D. Pierson Smela, Thomas H. H. Jordan, Kamesh Narasimhan, George M. Church
Summary: T-box riboswitches are a large family of tRNA-binding leader sequences that are crucial for gene regulation in many gram-positive bacteria. TBDB is an open-access database that contains a vast collection of T-box riboswitch sequences and provides structural annotations for this important family of regulatory RNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Gastroenterology & Hepatology
Clara Delaroque, Gary D. D. Wu, Charlene Compher, Josephine Ni, Lindsey Albenberg, Qing Liu, Yuan Tian, Andrew D. D. Patterson, James D. D. Lewis, Andrew T. T. Gewirtz, Benoit Chassaing
Summary: The study found that individual differences in diet and day-to-day variations in diet have a significant impact on the composition of the gut microbiota. Normalization of diet can reduce intra-individual variation and decrease the pro-inflammatory potential of the microbiota.
Article
Biochemistry & Molecular Biology
Liang Nie, Yujie Xiao, Tiantian Zhou, Haoqi Feng, Meina He, Qingyuan Liang, Kexin Mu, Hailing Nie, Qiaoyun Huang, Wenli Chen
Summary: This study reveals that the bacterial second messenger c-di-GMP regulates nitrate assimilation by binding to NasT, which inhibits the expression of key enzymes involved in nitrate assimilation, leading to nitrite accumulation in cells. The c-di-GMP-binding ability of NasT is conserved in other Pseudomonas species.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Microbiology
Sarah L. Gaffen, Partha S. Biswas
Summary: Recent research has found that commensal mucosa-associated gut fungi have a profound impact on host immunity, epithelial barrier function, and the regulation of social behavior through neuroimmunity. These effects are mediated by the activation of type 17 cytokines induced by fungi, which act on both epithelial cells and neurons.
CELL HOST & MICROBE
(2022)
Article
Biochemistry & Molecular Biology
Kan Gao, Aitak Farzi, Xueqin Ke, Yunxia Yu, Cailin Chen, Su Chen, Tengfei Yu, Haifeng Wang, Yanjun Li
Summary: Depression, associated with abnormalities in 5-HT metabolism, can be improved by certain probiotics. The L. lactis strain WHH2078 demonstrated antidepressant effects in mice with induced chronic unpredictable mild stress, through enhancing 5-HT metabolism and modulating gut microbiome composition.
Article
Biochemistry & Molecular Biology
Wei Liu, Taili Shao, Lei Tian, Zhengrui Ren, Lan Gao, Zhiyan Tang, Zheng Fang, Pingchuan Yuan, Chunyan Liu, Jikun Li, Guodong Wang, Jun Han
Summary: In this study, a homogeneous polysaccharide PCP1 was extracted and purified from Polygonatum cyrtonema Hua. The chemical structure analysis showed that PCP1 is mainly composed of fructose, glucose, and mannose. In vivo experiments demonstrated that PCP1 has potential therapeutic effects on non-alcoholic fatty liver disease (NAFLD) by mitigating liver pathological damage, improving abnormal lipid metabolism, promoting the production of short-chain fatty acids, and balancing the composition of the intestinal microbiota.