Biology subjects

Berks, B. C.

Publications and source records attributed to Berks, B. C..

7 recordsLinked to original sources

bioRxiv2026

Open filament tracks drive Bacteroidota gliding motility

Bacteria of the phylum Bacteroidota glide across surfaces using adhesins that attach to the substratum and are propelled along the cell body by an underlying track. The track is currently thought to form a single closed loop around the cell. Here we use 3D super-resolution tracking of single adhesin molecules in Flavobacterium johnsoniae to characterize adhesin movements in unprecedented detail. Our data overturn multiple aspects of the single closed loop model by showing that adhesins follow non-repeating trajectories that cross, make sharp turns, and exhibit reversals and circular paths. We develop a new model for Bacteroidota gliding in which the track network comprises multiple independently moving, open filaments. This supramolecular organization resembles that of other moving bacterial filaments such as MreB and FtsZ, suggesting that open filaments are a common organising principle in the bacterial cytoskeleton.

microbiology↗

bioRxiv2026

An expanded LPS translocon mediates surface lipoprotein export in the Bacteroidota

Cell surface lipoproteins (SLPs) play crucial roles in the pathogenesis and cell biology of gram-negative bacteria, yet the route by which they reach the cell surface has remained unknown except in special cases. Here we show that in Bacteroidota bacteria, a phylum that includes prominent human commensals and anaerobic pathogens, SLP export is carried out by the outer membrane lipopolysaccharide (LPS) translocon. Isolation and structural characterisation of LPS translocon complexes from two Bacteroidota species reveals that they are massively enlarged and elaborated relative to the Escherichia coli paradigm with up to eight additional subunits located within, and on either side of, the outer membrane. We establish a role for the universally conserved core LptD subunit and four of the additional Bacteroidota-specific subunits in SLP export. Expansion of the LPS translocon in the Bacteroidota may allow export of the unusually complex SLPs found in this phylum. Our discoveries raise the possibility that SLP export is a conserved second function of the LPS transport pathway across gram-negative bacteria.

microbiology↗

bioRxiv2025

Structure and substrate recognition by the Twin-arginine translocation (Tat) pathway core complex

The twin-arginine translocation (Tat) system is a mechanistically unique protein transport pathway moving folded proteins across membranes (1-4). It is found in all domains of life and is essential for plant photosynthesis and bacterial virulence(2, 5-7). A core complex composed of membrane proteins TatA, TatB, and TatC binds substrate proteins and then recruits additional TatA protomers to form the transport site(8-10). Here we present structures of resting and substrate-bound states of the Tat core complex together with biochemical and functional analysis. Substrate proteins associate with the core complex solely through their N-terminal signal peptides with their Tat targeting sequences making specific contacts with TatC and the peptide body clamped by TatB. The core complex contains highly tilted transmembrane helices that drive extreme local membrane thinning. Based on our results we propose a model for the early steps in Tat transport.

biochemistry↗

bioRxiv2025

Structure of the conjugation surface exclusion protein TraT

Conjugal transfer of plasmids between bacteria is a major route for the spread of antimicrobial resistance. Many conjugative plasmids encode exclusion systems that inhibit redundant conjugation. In incompatibility group F (IncF) plasmids surface exclusion is mediated by the outer membrane protein TraT. Here we report the cryoEM structure of the TraT exclusion protein complex from the canonical F plasmid of Escherichia coli. TraT is a hollow homodecamer shaped like a chefs hat. In contrast to most outer membrane proteins, TraT spans the outer membrane using transmembrane helices. We use a novel microscopy-based conjugation assay to probe the effects of directed mutagenesis on TraT. Our analysis provides no support for the idea that TraT has specific interactions with partner proteins. Instead, we infer that TraT is most likely to function by physical interference with conjugation.

microbiology↗

bioRxiv2025

A central, shared role for disulfide bonds in Bacteroidota protein transport and gliding motility

Bacteria of the phylum Bacteroidota are major human commensals and pathogens in addition to being abundant members of the wider biosphere. Bacteroidota move by gliding and they export proteins using the Type 9 Secretion System (T9SS). Here we discover that gliding motility and the T9SS share a novel mechanism of energisation in which outer membrane proteins are covalently attached by disulfide bonds to a moving internal track structure which propels them through the membrane. We determined the structure of a representative Bacteriodota mobile track by obtaining the cryoEM structure of a 3 MDa circular mini-track from Porphyromonas gingivalis. Our discoveries identify a novel mechanistic and evolutionary link between gliding motility and T9SS-dependent protein transport.

microbiology↗

bioRxiv2025

A new structural paradigm for outer membrane protein biogenesis in the Bacteroidota

In Gram-negative bacteria the outer membrane (OM) is the first line of defence against antimicrobial agents and immunological attacks. A key part of OM biogenesis is insertion of OM proteins (OMPs) by the {beta}-barrel-assembly machinery (BAM). Here we report the cryo-electron microscopy (cryoEM) structure of a BAM complex isolated from Flavobacterium johnsoniae, a member of the phylum Bacteroidota that includes key human commensals and major anaerobic pathogens. This BAM complex is radically different from the canonical Escherichia coli system and includes an extensive extracellular canopy that overhangs the substrate folding site and a subunit that inserts into the BAM pore. We find that two of the novel subunits involved in forming the extracellular canopy are essential for BAM function. For one of these subunits isolation of a suppressor mutation allows the separation of their essential and non-essential functions. The need for a highly remodelled and enhanced BAM complex reflects the unusually complex membrane proteins found in the OM of the Bacteroidota.

microbiology↗

bioRxiv2022

Structures of the Type IX Secretion/gliding motility motor from across the phylum Bacteroidetes

Gliding motility using cell surface adhesins and export of proteins by the Type IX Secretion System (T9SS) are two phylum-specific features of the Bacteroidetes. Both of these processes are energized by the GldLM motor complex which transduces the protonmotive force at the inner membrane into mechanical work at the outer membrane. We previously used cryo-electron microscopy to solve the structure of the GldLM motor core from Flavobacterium johnsoniae at 3.9 [A] resolution (Nat Microbiol (2021) 6: 221-233). Here we present structures of homologous complexes from a range of pathogenic and environmental Bacteroidetes species at up to 3.0 [A] resolution. These structures show that the architecture of the GldLM motor core is conserved across the Bacteroidetes phylum although there are species-specific differences at the N-terminus of GldL. The resolution improvements reveal a cage-like structure that ties together the membrane-proximal cytoplasmic region of GldL and influences gliding function. These findings add detail to our structural understanding of bacterial ion-driven motors that drive the T9SS and gliding motility. ImportanceMany bacteria in the Bacteroidetes phylum use the Type IX Secretion System to secrete proteins across their outer membrane. Most of these bacteria can also glide across surfaces using adhesin proteins that are propelled across the cell surface. Both secretion and gliding motility are driven by the GldLM protein complex which forms a nanoscale electrochemical motor. We used cryo-electron microscopy to study the structure of the GldLM protein complex from different species including the human pathogens Porphyromonas gingivalis and Capnocytophaga canimorsus. The organisation of the motor is conserved across species, but we find species-specific structural differences and resolve motor features at higher resolution. This work improves our understanding of the Type IX Secretion System, which is a virulence determinant in human and animal diseases.

biochemistry↗