title: Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12.
abstract: A barrier for horizontal gene transfer is high gene expression, which is metabolically expensive. Silencing of horizontally-acquired genes in the bacterium Escherichia coli is caused by the global transcriptional repressor H-NS. The activity of H-NS is enhanced or diminished by other proteins including its homologue StpA, and Hha and YdgT. The interconnections of H-NS with these regulators and their role in silencing gene expression in E. coli are not well understood on a genomic scale. In this study, we use transcriptome sequencing to show that there is a bi-layered gene silencing system - involving the homologous H-NS and StpA - operating on horizontally-acquired genes among others. We show that H-NS-repressed genes belong to two types, termed "epistatic" and "unilateral". In the absence of H-NS, the expression of "epistatically controlled genes" is repressed by StpA, whereas that of "unilaterally controlled genes" is not. Epistatic genes show a higher tendency to be non-essential and recently acquired, when compared to unilateral genes. Epistatic genes reach much higher expression levels than unilateral genes in the absence of the silencing system. Finally, epistatic genes contain more high affinity H-NS binding motifs than unilateral genes. Therefore, both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.
authors: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India.
authors: Rajalakshmi
authors: R
authors: Srinivasan
authors: Deepti
authors: D
authors: Chandraprakash
authors: Revathy
authors: R
authors: Krishnamurthi
authors: Parul
authors: P
authors: Singh
authors: Vittore F
authors: VF
authors: Scolari
authors: Sandeep
authors: S
authors: Krishna
authors: Aswin Sai Narain
authors: AS
authors: Seshasayee
mesh_terms: D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D004843:Epistasis, Genetic; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D036781:Fimbriae Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D020868:Gene Silencing; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D018832:Molecular Chaperones / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C529458:FimG protein, E coli; D018832:Molecular Chaperones; D012097:Repressor Proteins; C090104:StpA protein, E coli; C561315:YdgT protein, E coli; C079209:hha protein, E coli; D036781:Fimbriae Proteins