Biology subjects

Zenkin, N.

Publications and source records attributed to Zenkin, N..

3 recordsLinked to original sources

bioRxiv2026

Structural basis for the unexpected activity of rifamycin B against rifampicin-resistant RNA polymerase

Rifamycins inhibit bacterial transcription by targeting RNA polymerase (RNAP), but their clinical effectiveness is limited by the rapid emergence of resistance caused by mutations within the rifamycin-binding pocket. Rifamycin B (Rif B), one of the earliest discovered members of this antibiotic family and a precursor of clinically used derivatives, has remained poorly characterized because of its chemical instability and relatively weak antibacterial activity. Here, we revisit Rif B using biochemical and structural approaches. We show that Rif B remains sufficiently stable under assay conditions and retains inhibitory activity against RNAP variants carrying clinically relevant rifampicin-resistance mutations. We report the first crystal structure of Rif B and determine the structure of Rif B bound to bacterial RNAP. The structures reveal that the distinctive C-4 O-carboxymethyl substituent of Rif B forms an intramolecular interaction in the free molecule but establishes a salt bridge with fork loop 2 of the RNAP {beta}-subunit upon binding. This additional interaction explains the reduced sensitivity of Rif B to resistance-associated substitutions and identifies the C-4 position as an underexplored site for rational rifamycin modification. These findings redefine Rif B as a mechanistically distinct rifamycin scaffold and provide new insights for developing inhibitors targeting rifampicin-resistant RNAP.

biochemistry↗

bioRxiv2026

Transertion provides evidence for coupling of transcription and translation in Bacillus subtilis

In Gram-negative bacteria, co-translational insertion of membrane proteins into the plasma membrane may be coupled to ongoing transcription, a phenomenon known as transertion. Transertion results in a physical shift of the coding gene from the nucleoid towards the membrane and is one of the determinants of the shape of the nucleoid and placement of cell division in Gram-negative bacteria. In contrast, the existence of functional coupling of transcription and translation in Bacillus subtilis and potentially other Gram-positive bacteria has been questioned, suggesting that transertion may not happen. Here, by imaging vertically oriented B. subtilis cells, we show that the gene of a transmembrane protein changes its localization from inside the nucleoid to the plasma membrane upon induction of its transcription. Localization is restored to the nucleoid when induction of transcription has ceased. The shift of the gene towards the membrane is strictly dependent on transcription, its induction, translation and transmembrane nature of the coded protein. These results suggest that, at least, some principles of cellular regulation based on functional coupling of transcription and translation may be conserved between Gram-positive and Gram-negative bacteria.

molecular biology↗

bioRxiv2024

Conserved protein Seb1 that interacts with RNA polymerase II and RNA is a bona fide transcription elongation factor

Maturation of protein-coding precursor messenger RNA (pre-mRNA) is closely linked to RNA polymerase II (Pol II) transcription. However, the mechanistic understanding of how RNA processing is coordinated with transcription is incomplete. Conserved proteins interacting with the C-terminal domain of the largest catalytic subunits of Pol II and nascent RNA (CID-RRM factors) were demonstrated to play a role in mRNA 3-end processing and termination of Pol II transcription. Here, we employ a fully reconstituted system to demonstrate that fission yeast CID-RRM factor Seb1 acts as a bona fide elongation factor in vitro. Our analyses show that Seb1 exhibits context-dependent regulation of Pol II pausing, capable of either promoting or inhibiting pause site entry. We propose that CID-RRM factors coordinate Pol II transcription and RNA 3-end processing by modulating the rate of Pol II transcription.

molecular biology↗