Biology subjects

Lewis, P. J.

Publications and source records attributed to Lewis, P. J..

3 recordsLinked to original sources

bioRxiv2026

Structural basis of the nucleotide incorporation cycle of bacterial DNA polymerase III

Bacterial DNA polymerase III (PolIII) is the primary replicative polymerase responsible for faithful genome duplication, yet high-resolution structural snapshots of the enzyme during DNA synthesis and proofreading have remained elusive. Here we determine cryo-EM structures of the Escherichia coli PolIII core-clamp-DNA binary, ternary and proofreading complexes at 2.4-2.7 [A] resolution, revealing the structural basis of nucleotide selection, incorporation and proofreading. Binding of an incoming nucleotide expels the single-stranded template overhang from the polymerase central channel and induces a large rotation of the polymerase index finger, which closes around the incoming nucleotide to form a compact nascent base-pair-binding pocket. A conserved tyrosine on the finger stacks against the incoming nucleotide to impose stringent steric constraints that promote nucleotide selection, whereas a conserved histidine acts as a steric gate to exclude ribonucleotides. The proofreading structures capture key intermediates that reveal how PolIII transfers a mismatched primer terminus to the 3'-5' exonuclease active site and excises the misincorporated nucleotide while avoiding unnecessary degradation of correctly paired DNA. Together, these findings define the molecular mechanism by which the bacterial replicative polymerase couples rapid and processive DNA synthesis with exceptional replication fidelity.

biochemistry↗

bioRxiv2023

Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli

Ring-shaped DNA sliding clamps are essential for DNA replication and genome maintenance. Clamps need to be opened or trapped open and chaperoned onto DNA by clamp loader complexes (CLCs). Detailed understanding of the mechanisms by which CLCs open and place clamps around DNA remains limited. Here, we present a series of six structures of the Escherichia coli CLC bound to an open or closed clamp on and off a primer-template DNA that represent all intermediates in the clamp loading process. We show that the ATP-bound CLC first binds to a clamp, then constricts to hold onto it. The CLC then expands to open the clamp with a gap large enough for double-stranded DNA to enter. Upon binding to DNA, the CLC constricts slightly, allowing ATP hydrolysis and clamp closing around DNA. Although both yeast and E. coli CLCs open clamps by crab claw-like motions, they do it by the CLC expanding in opposite directions. These structures provide critical high-resolution snapshots of clamp loading by the E. coli CLC, revealing how the molecular machine works.

biochemistry↗

bioRxiv2016

In culture cross-linking of bacterial cells reveals proteome scale dynamic protein-protein interactions at peptide level

Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique inter-protein cross-linked peptides with less than a 1% false discovery rate by mass spectrometry and genome-wide data base searching. Nearly 60% of the inter-protein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the {delta} and {beta}' subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how {delta} might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth.

biochemistry↗