The transcription of many genes, particularly in prokaryotes, is controlled by transcription factors whose activity can be modulated by controlling their DNA binding affinity. Understanding the molecular mechanisms by which DNA binding affinity is regulated is important, but because forming definitive conclusions usually requires detailed structural information in combination with data from extensive biophysical, biochemical, and sometimes genetic experiments, little is truly understood about this topic. This review describes the biological requirements placed upon DNA binding transcription factors and their consequent properties, particularly the ways that DNA binding affinity can be modulated and methods for its study. What is known and not known about the mechanisms modulating the DNA binding affinity of a number of prokaryotic transcription factors, including CAP and lac repressor, is provided.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/bi400968e | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Evolutionary origins and functional diversification of Auxin Response Factors.
Nat Commun
December 2024
Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, the Netherlands.
The Auxin Response Factors (ARFs) family of transcription factors are the central mediators of auxin-triggered transcriptional regulation. Functionally different classes of extant ARFs operate as antagonistic auxin-dependent and -independent regulators. While part of the evolutionary trajectory to the present auxin response functions has been reconstructed, it is unclear how ARFs emerged, and how early diversification led to functionally different proteins.
View Article and Find Full Text PDFThe impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms.
NPJ Biofilms Microbiomes
December 2024
Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, 2200, Denmark.
The evolution of antimicrobial resistance (AMR) in biofilms, driven by mechanisms like oxidative stress, is a major challenge. This study investigates whether antioxidants (AOs) such as N-acetyl-cysteine (NAC) and Edaravone (ED) can reduce AMR in Pseudomonas aeruginosa biofilms exposed to sub-inhibitory concentrations of ciprofloxacin (CIP). In vitro experimental evolution studies were conducted using flow cells and glass beads biofilm models.
View Article and Find Full Text PDFCommunication between DNA polymerases and Replication Protein A within the archaeal replisome.
Nat Commun
December 2024
Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.
Replication Protein A (RPA) plays a pivotal role in DNA replication by coating and protecting exposed single-stranded DNA, and acting as a molecular hub that recruits additional replication factors. We demonstrate that archaeal RPA hosts a winged-helix domain (WH) that interacts with two key actors of the replisome: the DNA primase (PriSL) and the replicative DNA polymerase (PolD). Using an integrative structural biology approach, combining nuclear magnetic resonance, X-ray crystallography and cryo-electron microscopy, we unveil how RPA interacts with PriSL and PolD through two distinct surfaces of the WH domain: an evolutionarily conserved interface and a novel binding site.
View Article and Find Full Text PDFNesfatin-1 as a crucial mediator of glucose homeostasis in the reptile, Hemidactylus flaviviridis.
Sci Rep
December 2024
University of Jammu, Jammu and Kashmir, 180006, India.
Nesfatin-1 is a crucial regulator of energy homeostasis in mammals and fishes, however, its metabolic role remains completely unexplored in amphibians, reptiles, and birds. Therefore, present study elucidates role of nesfatin-1 in glucose homeostasis in wall lizard wherein fasting stimulated hepatic nucb2/nesfatin-1, glycogen phosphorylase (glyp), phosphoenolpyruvate carboxykinase (pepck), and fructose 1,6-bisphosphatase (fbp), while feeding upregulated pancreatic nucb2/nesfatin-1 and insulin, suggesting towards tissue-specific dual role of nesfatin-1 in glucoregulation. The glycogenolytic/gluconeogenic role of nesfatin-1 was further confirmed by an increase in media glucose levels along with heightened hepatic pepck and fbp expression and concomitant decline in liver glycogen content in nesfatin-1-treated liver of wall lizard.
View Article and Find Full Text PDFShort tandem repeats delineate gene bodies across eukaryotes.
Nat Commun
December 2024
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
Short tandem repeats (STRs) have emerged as important and hypermutable sites where genetic variation correlates with gene expression in plant and animal systems. Recently, it has been shown that a broad range of transcription factors (TFs) are affected by STRs near or in the DNA target binding site. Despite this, the distribution of STR motif repetitiveness in eukaryote genomes is still largely unknown.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!