Dominant negative autoregulation limits steady-state repression levels in gene networks

Abstract

Many transcription factors repress transcription of their own genes. Negative autoregulation has been shown to reduce cell-cell variation in regulatory protein levels and speed up the response time in gene networks. In this work we examined transcription regulation of the galS gene and the function of its product, the GalS protein. We observed a unique operator preference of the GalS protein characterized by dominant negative autoregulation. We show that this pattern of regulation limits the repression level of the target genes in steady states. We suggest that transcription factors with dominant negative autoregulation are designed for regulating gene expression during environmental transitions. A large class of transcription factors (TFs) responds to environmental or intracellularly synthesized signals and changes transcription of a gene set accordingly. In many cases TFs enhance (positive autoregulation) or inhibit (negative autoregulation) their own synthesis (8, 16). Autoregulation of TFs plays an important role in genetic networks. For example, positively autoregulated TFs are key elements of switches and memory devices, while negative autoregulation of a TF can provide stability and speed up response time (1, 2, 6, 9, 11, 15). In this work we study regulation of the galS gene and the function of its product, the Gal isorepressor (GalS) protein in Escherichia coli. GalS inhibits transcription of the galactose (gal) regulon promoters in E. coli by binding to 16-bp operator sequences in the cis-regulatory regions of the P1galE , PmglB , PgalP , PgalS , and PgalR promoters (14, 18). DNA binding by GalS is inhibited in the presence of the sugar d-galactose (19). Transcription of the galS gene is highly dependent on the cyclic AMP (cAMP) receptor protein (CRP), which in the presence of cAMP activates the PgalS promoter (17). Negative autoregulation of GalS has been demonstrated both in vivo and in vitro (14, 17). There are two operator sites in the galS gene, one upstream of the promoter (galS O E) and a second in the coding sequence (galS O I); however, the role of galS O I is unclear (10, 17) (Fig. 1). We measure transcription levels of the gal regulon promoters in an in vitro system in the presence of GalS and use mathematical modeling for analysis of results. We report that negative autoregulation dominates GalS function. The significance of dominant negative autoregulation in genetic networks is discussed.