Binding of the C-terminal domain of the alpha subunit of RNA polymerase to the phage mu middle promoter

Functional insights into Mycobacterium tuberculosis DevR-dependent transcriptional machinery utilizing Escherichia coli

DevR/DosR response regulator is believed to participate in virulence, dormancy adaptation and antibiotic tolerance mechanisms of Mycobacterium tuberculosis by regulating the expression of the dormancy regulon. We have previously shown that the interaction of DevR with RNA polymerase is essential for the expression of DevR-regulated genes. Here, we developed a M. tuberculosis-specific in vivo transcription system to enrich our understanding of DevR-RNA polymerase interaction. This in vivo assay involves co-transforming E. coli with two plasmids that express α, β, β' and σA subunits of M. tuberculosis RNA polymerase and a third plasmid that harbors a DevR expression cassette and a GFP reporter gene under the DevR-regulated fdxA promoter. We show that DevR-dependent transcription is sponsored exclusively by M. tuberculosis RNA polymerase and regulated by α and σA subunits of M. tuberculosis RNA polymerase. Using this E. coli triple plasmid system to express mutant variants of M. tuberculosis RNA polymerase, we identified E280 residue in C-terminal domain of α and K513 and R515 residues of σA to participate in DevR-dependent transcription. In silico modeling of a ternary complex of DevR, σA domain 4 and fdxA promoter suggest an interaction of Q505, R515 and K513 residues of σA with E178 and D172 residues of DevR and E471 of σA, respectively. These findings provide us with new insights into the interactions between DevR and RNA polymerase of M. tuberculosis which can be targeted for intercepting DevR function. Finally, we demonstrate the utility of this system for screening of anti-DevR compounds.

The phage Mu middle promoter Pm contains a partial UP element

There are three phases of transcription during lytic development of bacteriophage Mu: early, middle, and late. Transcription from the middle phase promoter P_m requires the activator protein Mor. In the presence of Mor, transcription from P_m is carried out by the Escherichia coli RNA polymerase holoenzyme containing σ⁷⁰. A Mor dimer binds to two 5-bp inverted repeats within a 16-bp element centered at −43.5 in P_m, replacing the normal −35 element contacted by RNA polymerase (RNAP). In this study random and targeted mutagenesis of the sequence upstream (−88 to −52) of the Mor binding site was performed to determine whether P_m also contains an UP element for binding of the RNAP α subunit, thereby stimulating transcription. The results demonstrated that mutations upstream of −57 had no effect on P_m activity in vivo, assayed by expression of lacZ fused downstream of a wild-type or mutant P_m. Mutations at positions −57 through −52 led to decreased transcription from P_m, consistent with the presence of an UP element. In DNase I footprinting and gel mobility shift assays, paired mutations at positions −55 and −54 did not affect Mor binding but decreased the synergistic binding of Mor with histidine tagged α (His-α), indicating that His-α binds to P_m in a sequence- and/or structure-specific manner. Taken together, these results demonstrate that P_m has a strong proximal UP element subsite, but lacks a distal subsite.

Genetic analysis of phage Mu Mor protein amino acids involved in DNA minor groove binding and conformational changes

Gene expression during lytic development of bacteriophage Mu occurs in three phases: early, middle, and late. Transcription from the middle promoter, P(m), requires the phage-encoded activator protein Mor and the bacterial RNA polymerase. The middle promoter has a -10 hexamer, but no -35 hexamer. Instead P(m) has a hyphenated inverted repeat that serves as the Mor binding site overlapping the position of the missing -35 element. Mor binds to this site as a dimer and activates transcription by recruiting RNA polymerase. The crystal structure of the His-Mor dimer revealed three structural elements: an N-terminal dimerization domain, a C-terminal helix-turn-helix DNA-binding domain, and a β-strand linker between the two domains. We predicted that the highly conserved residues in and flanking the β-strand would be essential for the conformational flexibility and DNA minor groove binding by Mor. To test this hypothesis, we carried out single codon-specific mutagenesis with degenerate oligonucleotides. The amino acid substitutions were identified by DNA sequencing. The mutant proteins were characterized for their overexpression, solubility, DNA binding, and transcription activation. This analysis revealed that the Gly-Gly motif formed by Gly-65 and Gly-66 and the β-strand side chain of Tyr-70 are crucial for DNA binding by His-tagged Mor. Mutant proteins with substitutions at Gly-74 retained partial activity. Treatment with the minor groove- and GC-specific chemical chromomycin A(3) demonstrated that chromomycin prevented His-Mor binding but could not disrupt a pre-formed His-Mor·DNA complex, consistent with the prediction that Mor interacts with the minor groove of the GC-rich spacer in the Mor binding site.