Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB

Abstract

RcsB is a highly conserved transcription regulator of the Rcs phosphorelay system, a complex two-component signal transduction system (N. Majdalani and S. Gottesman, Annu Rev Microbiol 59:379–405, 2005; A. J. Wolfe, Curr Opin Microbiol 13:204–209, 2010, https://doi.org/10.1016/j.mib.2010.01.002; D. J. Clarke, Future Microbiol 5:1173–1184, 2010, https://doi.org/10.2217/fmb.10.83). RcsB plays an important role in virulence and pathogenicity in human hosts by regulating biofilm formation. RcsB can regulate transcription alone or together with its auxiliary transcription regulators by forming heterodimers. This complexity allows RcsB to regulate transcription of more than 600 bacterial genes in response to different stresses (D. Wang et al., Mol Plant Microbe Interact 25:6–17, 2012, https://doi.org/10.1094/MPMI-08-11-0207). Despite increasing knowledge of RcsB importance, molecular mechanisms that drive the ability of RcsB to control transcription of a large number of genes remain unclear. Here, we present crystal structures of unphosphorylated RcsB in complex with the consensus DNA-binding sequence of 22-mer (DNA22) and 18-mer (DNA18) of the flhDC operon from Escherichia coli determined at 3.15- and 3.37-Å resolution, respectively. The results of our structural analysis combined with the results of in vitro binding assays provide valuable insights to the protein regulatory mechanism, demonstrate how RcsB recognizes target DNA sequences, and reveal a unique oligomeric state that allows RcsB to form homo- and heterodimers. This information will help us understand the complex mechanisms of transcriptional regulation by RcsB in bacteria.

An Intertwined Network of Regulation Controls Membrane Permeability Including Drug Influx and Efflux in Enterobacteriaceae

“…Detection of environmental change is the first adaptation/defense line of bacteria face to detrimental hazards to its basic physiological activities. Gram-negative bacteria have developed several systems that are able to sense the external medium modifications such as pH, osmotic strength, oxidative stress, nutrient starvation, toxic chemicals, and transfer the corresponding signal via transduction to appropriate internal regulators [ 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 ]. These regulators can directly or indirectly (regulation cascades) manage the expression of various components to adapt the bacterial membrane structure and composition allowing the bacteria to ensure their growth and survival [ 94 , 95 ].…”

“…The input and output domains of TCS (receptor domain of sensor protein and domain targeting DNA of the response regulator protein, respectively) being variable, TCS are able to recognize a variety of molecules and regulate a plethora of genes [ 97 ]. Additionally, multiple TCS may be active in the same bacterial cell [ 24 , 85 , 89 , 98 ].…”

“…It must be emphasized how the regulatory network is pleiotropic by (i) the large repertoire of signals triggering regulators, (ii) the substantial number of regulatory partners [ 89 , 118 , 119 ] acting at different levels (post-transcriptional, transcriptional, translational), in which most of them (iii) have multiple targets, and (iv) induce variable responses [ 83 , 110 ]; and (v) the overlap of the pathways leading to cross regulation (CpxAR and EnvZ/OmpR, CpxAR and σE, CpxAR and BaeSR, CpxAR and mar operon, σ E and PhoPQ, Rcs and PhoPQ, Rob and Mar etc.). The complexity of the regulatory network of a bacterium is much greater than what we know.…”

“…Additionally, this latter work allows to identify 25 genes regulated by ZraR, although the authors suggested that other response effectors in the ZraSR pathway may be involved [ 111 ]. Indeed, several studies point out that many signals/regulators/effectors remain to be discovered [ 89 , 101 , 111 , 118 ].…”

The spermidine acetyltransferase SpeG regulates transcription of the small RNA RprA

“…The Rcs phosphorelay is unusual, as the response regulator RcsB can form both a homodimer and a variety of heterodimers. The homodimer activates transcription of rprA [11, 12, 29], which encodes the small RNA regulator of the stationary phase sigma factor RpoS, and represses transcription of flhDC , which encodes the master regulator of the flagellar regulon [25, 30, 31]. To activate synthesis of the capsular exopolysacchararide colanic acid, RcsB forms a complex with a partner transcription regulator, RcsA, stabilizing the interaction between RcsB and a specific DNA binding site, the “RcsAB box” [32, 33].…”