The antibacterial peptide microcin J25 (MccJ25) inhibits transcription by bacterial RNA polymerase (RNAP). Biochemical results indicate that inhibition of transcription occurs at the level of NTP uptake or NTP binding by RNAP. Genetic results indicate that inhibition of transcription requires an extensive determinant, comprising more than 50 amino acid residues, within the RNAP secondary channel (also known as the "NTP-uptake channel" or "pore"). Biophysical results indicate that inhibition of transcription involves binding of MccJ25 within the RNAP secondary channel. Molecular modeling indicates that binding of MccJ25 within the RNAP secondary channel obstructs the RNAP secondary channel. We conclude that MccJ25 inhibits transcription by binding within and obstructing the RNAP secondary channel--acting essentially as a "cork in a bottle." Obstruction of the RNAP secondary channel represents an attractive target for drug discovery.

Microcins are a class of small (Ͻ10 kDa) ribosomally synthesized peptide antibiotics produced by Enterobacteriaceae (1). Some microcins undergo dramatic post-translational modifications by dedicated maturation machinery (2). Post-translationally modified microcins have unusual structures and target important cellular enzymes. The object of this study, microcin J25 (MccJ25), 3 is a 21-amino acid peptide that inhibits the activity of Gram-negative bacterial RNA polymerase (RNAP) and that inhibits growth of Gram-negative bacteria (primarily or exclusively Gram-negative enterics) (3, 4). MccJ25 has an unusual lariat-protoknot ("threaded lasso") structure, consisting of an eight-amino acid cycle with backbone-side chain lactam bond between the ␣-amino group of Gly 1 and the ␥-carboxyl group of Glu 8 , followed by a 13-amino acid tail that loops back and threads through the cycle (5-7). The threaded tail is trapped within the cycle by the aromatic side chains of MccJ25 residues Phe 19 and Tyr 20 , which straddle the cycle (5-8). The unusual lariat-protoknot structure of MccJ25 results in exceptionally high thermal stability and exceptionally high resistance to denaturation by chaotropes and organic solvents (4,8).MccJ25 is produced by bacteria containing a plasmid-borne mcjABCD biosynthetic gene cluster (9). Mature MccJ25 is produced from a 58-amino acid ribosomally synthesized precursor, McjA, the product of the mcjA gene (9). Amino acid residues that become part of Mutations that confer resistance to MccJ25 in nonproducing cells map to the rpoB and rpoC genes (12, 13), which encode the RNAP ␤ and ␤Ј subunits, respectively. RNAP purified from such rpoB or rpoC mutant cells is resistant to MccJ25 in vitro, establishing that RNAP is the functional cellular target of the drug (12). Amino acid substitutions in RNAP that lead to MccJ25 resistance involve residues located in the RNAP secondary channel, which mediates entry of transcription substrates, NTPs, to the RNAP active center. It has been proposed that MccJ25 inhibits transcription, at least in part, by binding within and obstructing the RNAP secondary channel, interfering with entry of . This proposal has received support from biochemical, kinetic, and single-molecule analyses as well as from structural modeling (13,14).The fact that MccJ25 is produced from a ribosomally synthesized precursor enables one to exploit the power of genetic engineering in order to produce a library of MccJ25 mutants that can be screened for desired biological properties. Here, we report the results of such an effort. We present an essentially complete collection of point mutations in the MccJ25 coding portion of the mcjA gene, and we determine the effects of amino acid substitutions resulting from these point mutations on production of MccJ25 (comprising synthesis of MccJ25 precursor, processing of MccJ25 precursor, export of mature MccJ25, and * This work was supported, in whole or in part, by National Institutes of Health Grants GM41376 (to R. H. E.) and GM64530 (to K. S.) and by a NI...

We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to but not overlapping the RNAP active center and stabilizes an RNAP-active-center conformational state with a straight-bridge helix. The results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations exist and that cycling between straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations is required for RNAP function. The results set bounds on models for RNAP function and suggest strategies for design of novel antibacterial agents.