Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU.
The histone-like protein HU is a highly abundant DNA architectural protein that is involved in compacting the DNA of the bacterial nucleoid and in regulating the main DNA transactions, including gene transcription. However, the coordination of the genomic structure and function by HU is poorly understood. Here, we address this question by comparing transcript patterns and spatial distributions of RNA polymerase in Escherichia coli wild-type and hupA/B mutant cells. We demonstrate that, in mutant cells, upregulated genes are preferentially clustered in a large chromosomal domain comprising the ribosomal RNA operons organized on both sides of OriC. Furthermore, we show that, in parallel to this transcription asymmetry, mutant cells are also impaired in forming the transcription foci-spatially confined aggregations of RNA polymerase molecules transcribing strong ribosomal RNA operons. Our data thus implicate HU in coordinating the global genomic structure and function by regulating the spatial distribution of RNA polymerase in the nucleoid.
Berger
Michael
M
School of Engineering and Science, Jacobs University, Campus Ring 1, D-28759 Bremen, Germany. m.berger@jacobs-university.de
Farcas
Anca
A
Geertz
Marcel
M
Zhelyazkova
Petya
P
Brix
Klaudia
K
Travers
Andrew
A
Muskhelishvili
Georgi
G
D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D002352:Carrier Proteins / Q000235:genetics; D002876:Chromosomes, Bacterial / Q000235:genetics / Q000502:physiology; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D008856:Microscopy, Fluorescence; D009154:Mutation / Q000235:genetics / Q000502:physiology; D009876:Operon / Q000235:genetics; D012329:RNA, Bacterial / Q000096:biosynthesis / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D018741:Replication Origin / Q000235:genetics / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
D001426:Bacterial Proteins; D002352:Carrier Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C541388:HupB protein, E coli; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D014157:Transcription Factors; C040330:histone-like protein HU, bacteria; C490937:hupA protein, E coli; D012321:DNA-Directed RNA Polymerases