ReviewJournal of bacteriology2024
Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma.
Review in Journal of bacteriology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The shared evolutionary capacities of plasmids and extrachromosomal DNA.Nature reviews. Genetics · 2026Review
- Dual Role of Small Noncoding RNA and Hfq in Bacterial DNA Compaction: A New Perspective on Nucleoid Architecture.ACS omega · 2026Article
- Bacterial 3D genome architecture: organization, regulation, and synthetic biology applications.Genome biology · 2026Review
- Ultrastructural Study of the Effects of Hybrid Compounds of Natural Monoterpene Carvacrol and Synthetic Cationic Amphiphile DLInternational journal of molecular sciences · 2026Article
- Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics, and organization.Nucleic acids research · 2026Article
- The chromosomal origin of replication as the basis for the spatio-temporal biology of bacteria.Frontiers in microbiology · 2026Review
- Abundant positively-charged proteins underlie JCVI-Syn3A's expanded nucleoid and ribosome distribution.PLoS computational biology · 2026Article
- Omadacycline Pharmacokinetics: Characteristics, Contributing Factors, and Clinical Significance.Drugs in R&D · 2025Review
- Dps binds and protects DNA in starvedbioRxiv : the preprint server for biology · 2025Article
- Nucleoid structure and dynamics influence natural chromosomal transformation in Bacillus subtilis: the role of EbfC.Nucleic acids research · 2025Article
- Fixation Method Determines the Ultrastructure of the Nucleoid in Pseudomonas aeruginosa and Staphylococcus aureus.Bulletin of experimental biology and medicine · 2025Article
- UV induces codirectional replication-transcription conflicts and an alternative DnaA-dependent replication origin in the rnhAB mutants of Escherichiacoli.Nucleic acids research · 2025Article
- Review
- Nucleolar origins: challenging perspectives on evolution and function.Open biology · 2025Review
- Amyloid-like DNA bridging: a new mode of DNA shaping.Nucleic acids research · 2025Article
- CRISPR/Cas9-mediated genomic insertion of functional genes intoMicrobiology spectrum · 2025Article
- Kinetic Features of Degradation of R-Loops by RNase H1 fromInternational journal of molecular sciences · 2024Article
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Authors and funding
1 author.
Funding
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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