Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

Key Points The bacterial nucleoid is dynamic in nature and undergoes changes in its local and global structure as a result of DNA replication, DNA recombination and gene expression. Nucleoid-associated proteins (NAPs) contribute to both the organization of the nucleoid and the control of gene expression, and it is becoming evident that NAPs and transcription act in concert to confer structure on the bacterial genome. NAPs vary in the manner in which they interact with DNA, and their different binding modes facilitate positive or negative influences on transcription and also have different effects on the shape of the genetic material in the nucleoid. The bending, wrapping and bridging of DNA by NAPs contribute to the development of simple regulatory switches that control gene expression and recombination. Some transcription factors such as cyclic AMP–cAMP regulatory protein (Crp), which have been classified previously as conventional transcription factors that make highly specific contacts with RNA polymerase to control transcription initiation, have been found to bind far more widely in the genome than was previously believed. This suggests that the boundary between NAPs and at least some transcription factors may be blurred and that bacteria possess a population of different DNA-binding proteins with a spectrum of DNA-binding activities. Recent insights into the biology of NAPs, their roles in gene regulation and their relationships with horizontally acquired DNA are deepening our understanding of the contributions that NAPs have made, and are still making, to the evolution of the nucleoid and to the operations of the gene expression programmes therein. Nucleoid-associated proteins (NAPs) bind to the bacterial chromosome and alter its dynamics, maintaining nucleoid structure. In this Review, Dillon and Dorman examine the range of proteins in the ever-growing NAP family and their contributions to the regulation of nucleoid structure and gene expression. Emerging models of the bacterial nucleoid show that nucleoid-associated proteins (NAPs) and transcription contribute in combination to the dynamic nature of nucleoid structure. NAPs and other DNA-binding proteins that display gene-silencing and anti-silencing activities are emerging as key antagonistic regulators of nucleoid structure. Furthermore, it is becoming clear that the boundary between NAPs and conventional transcriptional regulators is quite blurred and that NAPs facilitate the evolution of novel