Common throughout life is the need to compact and organize the genome. Possible mechanisms involved in this process include supercoiling, phase separation, charge neutralization, macromolecular crowding, and nucleoid-associated proteins (NAPs). NAPs are special in that they can organize the genome at multiple length scales, and thus are often considered as the architects of the genome. NAPs shape the genome by either bending DNA, wrapping DNA, bridging DNA, or forming nucleoprotein filaments on the DNA. In this mini-review, we discuss recent advancements of unique NAPs with differing architectural properties across the tree of life, including NAPs from bacteria, archaea, and viruses. To help the characterization of NAPs from the ever-increasing number of metagenomes, we recommend a set of cheap and simple in vitro biochemical assays that give unambiguous insights into the architectural properties of NAPs. Finally, we highlight and showcase the usefulness of AlphaFold in the characterization of novel NAPs.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1111/mmi.15298 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
In situ architecture of a nucleoid-associated biomolecular co-condensate that regulates bacterial cell division.
Proc Natl Acad Sci U S A
January 2025
Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany.
In most bacteria, cell division depends on the tubulin-homolog FtsZ that polymerizes in a GTP-dependent manner to form the cytokinetic Z-ring at the future division site. Subsequently, the Z-ring recruits, directly or indirectly, all other proteins of the divisome complex that executes cytokinesis. A critical step in this process is the precise positioning of the Z-ring at the future division site.
View Article and Find Full Text PDFSpatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans.
J Biol Chem
December 2024
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China. Electronic address:
Article Synopsis
- Deinococcus radiodurans is a hardy microorganism known for its ability to survive extreme radiation and chemical damage, largely due to its advanced DNA repair skills.
- Researchers used chromosome conformation capture (3C) technology to analyze the 3D structure of its genome and how UV irradiation affects chromosome organization.
- The study found that UV exposure leads to reduced chromosome interactions and larger chromosomal domains, revealing insights into how a protein called DrEbfC regulates gene expression and helps the organism cope with environmental stresses.
Oligomerization-mediated phase separation in the nucleoid-associated sensory protein H-NS is controlled by ambient cues.
Protein Sci
January 2025
Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
H-NS, a nucleoid-associated protein (NAP) from enterobacteria, regulates gene expression by dynamically transducing environmental cues to conformational assembly and DNA binding. In this work, we show that H-NS from Escherichia coli, which can assemble into octameric and tetrameric oligomerization states, forms spontaneous micron-sized liquid-like condensates with DNA at sub-physiological concentrations in vitro. The heterotypic condensates are metastable at 298 K, partially solubilizing with time, while still retaining their liquid-like properties.
View Article and Find Full Text PDFGenome-wide mapping of spontaneous DNA replication error-hotspots using mismatch repair proteins in rapidly proliferating Escherichia coli.
Nucleic Acids Res
December 2024
Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014 Paris, France.
Article Synopsis
- The study examines how spontaneous replication errors occur in the E. coli genome despite mechanisms meant to prevent them.
- Researchers identified specific hotspots for these errors, linked to factors such as DNA stability, sequence types that cause slippage, and structures that can stall DNA replication.
- Findings suggest that hotspots are associated with certain proteins, gene expression levels, and single-stranded DNA, highlighting complex interactions that affect the accuracy of genetic information transmission.
cells advance into phase-separated (biofilm-simulating) extracellular polymeric substance containing DNA, HU, and lipopolysaccharide.
J Bacteriol
November 2024
Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Punjab, India.
Unlabelled: We have previously shown that the nucleoid-associated protein, HU, uses its DNA-binding surfaces to bind to bacterial outer-membrane lipopolysaccharide (LPS), causing HU to act as a glue aiding the adherence of DNA to bacteria, e.g., in biofilms.
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!