title: The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia.
abstract: Dan is a transcription factor that regulates the ttd operon encoding tartrate dehydratase. During anaerobic conditions, its copy number increases by 100-fold, making Dan an abundant nucleoid-associated protein. However, little is known about the mode of Dan-DNA interaction. To understand its cellular functions, we used single-molecule manipulation and imaging techniques to show that Dan binds cooperatively along DNA, resulting in formation of a rigid periodic nucleoprotein filament that strongly restricts accessibility to DNA. Furthermore, in the presence of physiologic levels of magnesium, these filaments interact with each other to cause global DNA condensation. Overall, these results shed light on the architectural role of Dan in the compaction of Escherichia coli chromosomal DNA under anaerobic conditions. Formation of the nucleoprotein filament provides a basis in understanding how Dan may play roles in both chromosomal DNA protection and gene regulation.
authors.affiliation: National University of Singapore, Graduate School for Integrative Sciences and Engineering, Singapore.
authors.forename: Ci Ji
authors.initials: CJ
authors.lastname: Lim
authors.forename: Sin Yi
authors.initials: SY
authors.lastname: Lee
authors.forename: Jun
authors.initials: J
authors.lastname: Teramoto
authors.forename: Akira
authors.initials: A
authors.lastname: Ishihama
authors.forename: Jie
authors.initials: J
authors.lastname: Yan
mesh_terms: D000693:Anaerobiosis; D002876:Chromosomes, Bacterial; D004247:DNA / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000378:metabolism* / Q000648:ultrastructure*; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000378:metabolism* / Q000648:ultrastructure*; D015636:Magnesium Chloride / Q000737:chemistry; D009698:Nucleoproteins / Q000378:metabolism* / Q000648:ultrastructure*
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D009698:Nucleoproteins; C550806:TtdR protein, E coli; D015636:Magnesium Chloride; D004247:DNA