nucleoid

The nucleoid is the irregularly shaped region within a prokaryotic cell where the genetic material is located. Unlike the eukaryotic nucleus, it is not enclosed by a membrane. In most bacteria, the nucleoid contains a single circular chromosome and may also house small DNA molecules called plasmids. Some bacteria possess more complex genome architectures, including multiple chromosomes or megaplasmids, but even a simple genome is highly organized within the nucleoid.

DNA in the nucleoid is highly compacted and organized into looped domains. This organization is achieved without a membrane-bound nucleus through supercoiling, macromolecular crowding, and the action of nucleoid-associated proteins (NAPs) such as HU, IHF, Fis, and H-NS, as well as histone-like proteins in some species. Topoisomerases and DNA gyrase regulate supercoiling levels, enabling dynamic changes during replication and transcription.

DNA replication starts at the origin of replication (oriC) and proceeds bidirectionally. Transcription and translation are coupled in many bacteria and occur in the vicinity of the nucleoid. Nucleoid structure influences gene expression, DNA accessibility, and the timing of replication. During cell division, the nucleoid is compacted and partitioned to daughter cells via partitioning systems (ParABS in many species) and nucleoid occlusion mechanisms that coordinate chromosome segregation with cytokinesis.

Archaea possess a nucleoid with some similarities to bacterial nucleoids, and many archaeal species use histone-like proteins to package DNA. Overall, the nucleoid reflects a balance between compaction and accessibility, enabling efficient control of gene expression in response to cellular conditions.