title: Transcription-coupled nucleoid architecture in bacteria.
abstract: The circular bacterial genome DNA exists in cells in the form of nucleoids. In the present study, using genetic, molecular and structural biology techniques, we show that nascent single-stranded RNAs are involved in the step-wise folding of nucleoid fibers. In Escherichia coli, RNase A degraded thicker fibers (30 and 80 nm wide) into thinner fibers (10 nm wide), while RNase III and RNase H degraded 80-nm fibers into 30-nm (but not 10-nm) fibers. Similarly in Staphylococcus aureus, RNase A treatment resulted in 10-nm fibers. Treatment with the transcription inhibitor, rifampicin, in the absence of RNase A changed most nucleoid fibers to 10-nm fibers. Proteinase-K treatment of nucleoids exposed DNA. Thus, the smallest structural unit is an RNase A-resistant 10-nm fiber composed of DNA and proteins, and the hierarchical structure of the bacterial chromosome is controlled by transcription itself. In addition, the formation of 80-nm fibers from 30-nm fibers requires double-stranded RNA and RNA-DNA hetero duplex. RNA is evident in the architecture of log-phase uncondensed and stationary-phase condensed nucleoids.
authors: Laboratory of Plasma Membrane and Nuclear Signaling, Kyoto University, Graduate School of Biostudies, Yoshidahonmachi, Sakyo-ku, Kyoto 606-8501, Japan. ohniwa@lif.kyoto-u.ac.jp
authors: Ryosuke L
authors: RL
authors: Ohniwa
authors: Kazuya
authors: K
authors: Morikawa
authors: Sayaka L
authors: SL
authors: Takeshita
authors: Joongbaek
authors: J
authors: Kim
authors: Toshiko
authors: T
authors: Ohta
authors: Chieko
authors: C
authors: Wada
authors: Kunio
authors: K
authors: Takeyasu
mesh_terms: D001419:Bacteria / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D004269:DNA, Bacterial / Q000235:genetics; D004867:Equipment Design; D004926:Escherichia coli / Q000201:enzymology*; D015964:Gene Expression Regulation, Bacterial; D018625:Microscopy, Atomic Force / Q000295:instrumentation* / Q000379:methods; D008954:Models, Biological; D008957:Models, Genetic; D012313:RNA / Q000737:chemistry; D012259:Ribonuclease, Pancreatic / Q000737:chemistry; D013211:Staphylococcus aureus / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012313:RNA; D004247:DNA; D012259:Ribonuclease, Pancreatic