Bacterial Systems Biology: Genome, Transcriptome, Translatome, and Interactome

Over the past decade or so, dramatic developments in our ability to experimentally determine the contents and functions of genomes have taken place. In particular, high-throughput sequencing technologies are now inspiring a new understanding of the bacterial genome on a global scale. Bacterial genomes are organized by structural and functional elements, including promoters, transcription start and termination sites, open reading frames, regulatory noncoding regions, untranslated regions and transcription units. Thus, identification of those genomic elements is prerequisite for understanding the complete regulatory network of a bacterial cell. Here, we show the architecture of bacterial genome and gene expression patterns at transcriptional and translational level along with different developmental phases, by integrating genome-wide data of transcription start sites (TSSs), mRNA abundance and ribosome-protected mRNA fragment (RPF) abundance. Also, we disclosed the dynamics of transcription using ChIP-exo data with extremely high resolution of single base, together with ChIP-seq and RNA-seq data. The mobility of RNAP holoenzyme at transcription initiation was elucidated through genome-scale scanning for association of RNAP and sigma factor with genome. Thus, we offer comprehensive information on genome architecture, and transcriptional and translational gene expression patterns that allows better understanding of bacterial cells.