Nucleoids

Nucleoids are DNA–protein complexes that organize and package genetic material in cells where there is no membrane-bound nucleus. The term is used for the region containing chromosomal DNA in bacteria and many archaea, as well as for similarly organized genomes inside mitochondria and chloroplasts. In all cases, nucleoids serve to compact DNA, protect it, and coordinate replication, transcription, and repair processes.

In bacteria, the nucleoid region is not enclosed by a membrane. Most bacteria carry a single circular chromosome, sometimes with additional plasmids. DNA compaction is achieved with nucleoid-associated proteins (NAPs) such as HU, H-NS, Fis, and IHF, along with topoisomerases and structural maintenance of chromosomes (SMC) proteins. The genome is organized into looped, dynamic domains, aided by supercoiling and macromolecular crowding. Replication and transcription occur within the nucleoid, and transcription–translation coupling is common in growing cells.

In archaea, nucleoids resemble bacterial ones but rely on histone-like proteins and Alba to compact DNA, reflecting distinct evolutionary lineages of chromosome organization.

In mitochondria and chloroplasts, nucleoids are suborganellar DNA–protein complexes containing multiple copies of the organellar genome and associated factors necessary for replication, transcription, and maintenance. Mitochondrial nucleoids commonly include proteins such as TFAM, mtSSB, TWINKLE, and POLG; chloroplast nucleoids contain a set of organelle-specific nucleoid proteins and transcription components. These nucleoids are dynamic, distributed within the organelle, and act as functional units of genome inheritance and expression.

Overall, nucleoids unify the theme of genome organization across diverse cellular contexts, balancing compaction with accessibility for genetic function.