Structural basis for converting a general transcription factor into an operon-specific virulence regulator

Abstract

RfaH, a paralog of the general transcription factor NusG, is recruited to elongating RNA polymerase at specific regulatory sites. The X-ray structure of Escherichia coli RfaH reported here reveals two domains. The N-terminal domain displays high similarity to that of NusG. In contrast, the alpha-helical coiled-coil C domain, while retaining sequence similarity, is strikingly different from the beta barrel of NusG. To our knowledge, such an all-beta to all-alpha transition of the entire domain is the most extreme example of protein fold evolution known to date. Both N domains possess a vast hydrophobic cavity that is buried by the C domain in RfaH but is exposed in NusG. We propose that this cavity constitutes the RNA polymerase-binding site, which becomes unmasked in RfaH only upon sequence-specific binding to the nontemplate DNA strand that triggers domain dissociation. Finally, we argue that RfaH binds to the beta' subunit coiled coil, the major target site for the initiation sigma factors.

Figure 1. Structure of the RfaH Protein

(A) The overall structure. (B) Stereo view of the RfaH interdomain interface. All structural figures were prepared using the programs MOLSCRIPT, BOBSCRIPT, and Raster3D (Esnouf, 1999; Kraulis, 1991; Merrit and Bacon, 1997).

Figure 2. Comparison of the RfaH and NusG Structures

(A) Superposition of the RfaH and NusG N domains. (B) The overall structure of the NusG C domain. (C) Sequence alignment of the RfaH and NusG proteins built with DNA Star; the bar height indicates residue conservation. The conserved hydrophobic residues are highlighted in yellow; those lining the hydrophobic cavities of the N domains are additionally boxed. The secondary structure elements in A. aeolicus NusG and E. coli RfaH are shown above and below the alignment, respectively, and colored as in (A) and (B). The vertical black arrow indicates the position of a large insertion in A. aeolicus NusG.

Figure 3. Domain Opening Is Required for RfaH Function

(A) A disulfide bond engineered between the N- and C-domain residues 51 and 139; the interdomain linker absent from the structure is shown by a dashed line. (B) A 12% denaturing protein gel loaded with reduced (left) and oxidized (right) forms of RfaH^51C,139C (see the Experimental Procedures for details); the sizes of molecular weight markers are shown on the right. (C) Transcriptional phenotypes of RfaH^51C,139C. (Top) Transcript generated from the T7A1 promoter on a linear pIA449 template; transcription start site (+1), positions of ops and trp pause sites, his terminator, and run-off are indicated. (Bottom) Halted radiolabeled G37 TECs were preincubated with RfaH^51C,139 in reduced (SH HS), oxidized (S-S), oxidized state reduced with DTT (S-S + DTT), or storage buffer (none) for 5 min at 37°C, and then challenged with rifampicin at 25 μg/ml and NTPs (10 μM GTP and 150 μM ATP, CTP, and UTP). Aliquots were withdrawn at times ranging from 15 to 1200 s, followed by the 200 μM GTP chase for 300 s, and analyzed on 8% denaturing gels. (D) Quantification of the fraction of RNA at the ops (transcript position C45, left) and the trp (transcript position U124, right) pause sites from the data shown in (C). Fraction refers to the ratio of product at pause site to the sum of all products resulting from elongation of TEC halted at G37. The symbols are color-coded as in (C).

Figure 4. The N Domain Mediates the RfaH Effect on Elongation

(A) The pIA750-encoded protein designed to purify the C domain (black rectangle) of RfaH contained the TEV protease site (gray oval) in the linker between the two domains and the His₆ tag (red rectangle) fused to the N domain, whereas pIA777-encoded protein that was used to purify the N domain (white rectangle) had His₆ tag fused to the C domain. (B) SDS-PAGE gel of 750 and 777 proteins after TEV protease digestion (1 and 3, respectively) and absorption to Ni-Sepharose (2 and 4, respectively). The digested products are presented schematically as in (A). (C and D) In vitro transcription assays were performed similarly to those described in the Figure 3 legend on templates containing canonical (C) or scrambled (D) opsP pause sites (Artsimovitch and Landick, 2002) and a hairpin-dependent pause site hisP in the absence of RfaH (left panels), in the presence of full-length RfaH (middle panels) and purified N domain (right panels). Quantification of the fraction of RNA at the hisP site is shown below with the symbols color-coded to match labels for each gel panel; quantification of the opsP RNA is shown in Figure S4.

Figure 5. The Tip of the β′CC Is Required for RfaH Action

In vitro analysis of transcript elongation by the altered RNAP enzyme, in which the residues within the gray box were substituted with four glycines, on the template shown in Figure 4C. The assays were done in the absence of RfaH (left panel), in the presence of full-length RfaH (middle panel), and with the purified N domain (right panel). Quantification and comparison with the wild-type RNAP are presented in Figure S5.

Figure 6. The Model of RfaH Recruited to the TEC

(A) Overall model is presented in two distinct orientations. The RNAP is shown in gray with the β′CC (the RfaH-binding site) highlighted in magenta. The color scheme for the RfaH N and C domains is the same as in Figure 1. The RNAP active site is marked by the Mg²⁺ ion (magenta sphere). The template DNA, the nontemplate DNA, and the RNA transcript are colored in red, green, and yellow, respectively. (B) The close-up stereo view of RfaH bound to the β′CC. The side chains forming the intermolecular hydrophobic core are represented by the balls-and-sticks model (blue and magenta for the RfaH and β′CC, respectively). The nontemplate strand nucleotides adjacent to RfaH in the TEC model are shown in green and are numbered with respect to the position of the acceptor template base (register n). The cluster of the RfaH residues that confer defects in the ops DNA binding is colored in red. (C) Transcript elongation on pIA349 template (Figure 4C) by RNAPs containing I290R or I291R substitutions at the tip of the β′CC in the absence (left panels) or in the presence (right panels) of full-length RfaH. Quantification is presented in Figure S6.