Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene's numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9262627 | PMC |
| http://dx.doi.org/10.1093/nar/gkac540 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Development of triaryl antimicrobials by scaffold hopping from an aminopropanol hit targeting bacterial RNA polymerase-NusG interactions.
J Enzyme Inhib Med Chem
December 2025
State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China.
Bacterial RNA polymerase (RNAP) requires the NusG factor to facilitate transcription, with the RNAP clamp-helix domain (CH) serving as the primary binding site for NusG and representing a promising target for antimicrobial intervention. In previous work, we unprecedentedly developed a pharmacophore model based on key clamp-helix residues (R270, R278, R281) at RNAP CH essential for NusG binding, which led to the identification of a hit compound exhibiting modest antimicrobial activity against . In this study, we designed a new class of triaryl inhibitors via scaffold hopping, substituting the linear structure of the hit compound with a benzene ring.
View Article and Find Full Text PDFInorganic carbon levels regulate growth via SigC signaling cascade in cyanobacteria.
New Phytol
September 2025
Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, FI-20014, Finland.
Cyanobacterial growth depends on inorganic carbon (Ci; CO and bicarbonate) concentration, but mechanism(s) adjusting photosynthesis and growth according to Ci remain unclear. ΔrpoZ cells lacking the ω subunit of the RNA polymerase (RNAP) show a unique high-CO lethal phenotype in Synechocystis sp. PCC 6803.
View Article and Find Full Text PDFVoltammetric Sensor for Naproxen Enantiomers Based on a Paste Electrode Modified With a Chiral Nickel(II) Complex.
Chirality
February 2025
A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS), Moscow, Russian Federation.
An enantioselective voltammetric sensor (EVS) comprising a paste electrode made of graphitized thermal Carboblack C (CBPE) modified with a Ni(II) complex based on (S)-(2-aminomethyl)pyrrolidine and 3,5-di-tert-butylsalicylaldehyde was developed for the recognition and determination of naproxen (Nap) enantiomers. The proposed sensor was characterized by scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS-SEM), Fourier-transform infrared spectroscopy (FT-IR), molecular dynamics and quantum chemical simulations, electrochemical impedance spectroscopy (EIS), and cyclic voltammetry (CV) methods. Using the differential pulse voltammetry (DPV), the CBPE@(S)-Ni sensor was found to have good selectivity for Nap enantiomers (i/i = 1.
View Article and Find Full Text PDFCreating a System of Dual Regulation of Translation and Transcription to Enhance the Production of Recombinant Protein.
Biotechnol J
December 2024
School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu, China.
When constructing cell factories, it is crucial to reallocate intracellular resources towards the synthesis of target compounds. However, imbalanced resource allocation can lead to a tradeoff between cell growth and production, reducing overall efficiency. Reliable gene expression regulation tools are needed to coordinate cell growth and production effectively.
View Article and Find Full Text PDFDoes the herbicide napropamide exhibit enantioselective effects across genus plasmid transfer from Escherichia coli to Bacillus subtilis?
J Hazard Mater
February 2025
Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, China. Electronic address:
Article Synopsis
- - The study highlights the urgent issue of antibiotic resistance gene (ARG) spread in the environment, focusing on the impact of the herbicide napropamide (NAP) on plasmid transfer between bacteria.
- - It found that R-NAP significantly enhances plasmid transfer efficiency from E. coli to Bacillus subtilis compared to its S-enantiomer, particularly at a concentration of 5 mg/L, while also affecting bacterial structures and increasing membrane permeability.
- - The research identifies specific genes involved in this transfer and suggests that careful management of herbicides like R-NAP is necessary in agricultural settings to prevent the spread of ARGs, particularly in fields treated with livestock manure.