| The high information density of prokaryotic genomes requires that transcription terminate precisely at operon ends in order to avoid interference with neighboring transcription units. Both intrinsic and Rho-dependent termination signals are found at the ends of operons. We used chemical and genetic inhibition of Rho function in microarray experiments to assess the role of Rho and termination factors NusA and NusG in transcription regulation on a genome-wide basis. Our results indicate that inhibition of Rho by bicyclomycin (BCM) strongly affects the expression of most E. coli genes on a pervasive scale, in particular, it derepresses genes encoded by defective prophages and recently-acquired portions of the genome. This preference in the targets of Rho was observed in both the laboratory K-12 strain MG1655 as well as the enterohemorrhagic strain EDL933 serotype O157:H7. The upregulated genes are characterized by AT-rich sequence and low codon usage optimality. We extended our studies to strain MDS42, in which all prophages, transposons, and most genes horizontally-transferred into the genome of K-12 (663 kb, or 14%) were deleted. This strain was partially resistant to treatment with bicyclomycin and could sustain deletion of termination factors NusA and NusG. Proteomic analysis using difference gel electrophoresis demonstrates that during Rho inhibition by bicyclomycin the cell's protein complement remains relatively unperturbed, but that an anaerobic response is induced. We conclude that Rho factor functions globally to maintain transcriptional boundaries, regulate DNA acquired by horizontal transfer, and match transcriptional output to translational needs. |
