Biology subjects

Parrell, D.

Publications and source records attributed to Parrell, D..

4 recordsLinked to original sources

bioRxiv2025

Structural and Binding Properties of Dps: A Nucleoid Associated Protein

Prokaryotic chromosomal DNA is compacted and protected by nucleoid-associated proteins (NAPs). Among these, the DNA-binding proteins from starved cells (Dps) combine ferroxidase activity with nonspecific DNA binding to form dodecameric assemblies that condense and safeguard the genome under stress. Here, we present an integrated structural and biophysical analysis of Escherichia coli (E. coli) Dps across a pH range from 3 to 11, combining (i) single-particle cryo-EM reconstructions at [~]1.75 [A] resolution, (ii) adaptive Poisson-Boltzmann electrostatic modelling, (iii) electrophoretic mobility shift assays (EMSAs) on a 448 bp DNA fragment, and (iv) cryo-electron tomography (cryo-ET) of Dps-DNA assemblies. Through this analysis, we show that (1) the canonical ferritin-like fold is maintained at all pH values; (2) surface electrostatics shift from highly positive to net negative as the pH increases, modulating DNA affinity (EC50 values of 73.4 nM at the lowest measurement of pH 5, to 815.5 nM at the highest measurement of pH 11); and (3) short-fragment Dps-DNA complexes form amorphous [~]50 nm globular or tubular complexes rather than lattice co-crystals observed on kilobase-length DNA scaffolds. The findings reveal a possible two-stage assembly model, in which protonation-driven nucleation occurs via the Dps N-terminal lysine residues, followed by lattice ordering on long DNA. Our results further define Dps as a pH-responsive nucleoid compaction factor in bacteria.

biophysics↗

bioRxiv2023

Atomic-level architecture of Caulobacter crescentus flagellar filaments provide evidence for multi-flagellin filament stabilization

Flagella are dynamic, ion-powered machines with assembly pathways that are optimized for efficient flagella production. In bacteria, dozens of genes are coordinated at specific times in the cell lifecycle to generate each component of the flagellum. This is the case for Caulobacter crescentus, but little is known about why this species encodes six different flagellin genes. Furthermore, little is known about the benefits multi-flagellin species possess over single flagellin species, if any, or what molecular properties allow for multi-flagellin filaments to assemble. Here we present an in-depth analysis of several single flagellin filaments from C. crescentus, including an extremely well-resolved structure of a bacterial flagellar filament. We highlight key molecular interactions that differ between each bacterial strain and speculate how these interactions may alleviate or impose helical strain on the overall architecture of the filament. We detail conserved residues within the flagellin subunit that allow for the synthesis of multi-flagellin filaments. We further comment on how these molecular differences impact bacterial motility and highlight how no single flagellin filament achieves wild-type levels of motility, suggesting C. crescentus has evolved to produce a filament optimized for motility comprised of six flagellins. Finally, we highlight an ordered arrangement of glycosylation sites on the surface of the filaments and speculate how these sites may protect the {beta}-hairpin located on the surface exposed domain of the flagellin subunit.

biophysics↗

bioRxiv2022

Correlative cryogenic montage electron tomography for comprehensive in-situ whole-cell structural studies

Imaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here, we present robust tools for montage electron tomography tailored for vitrified specimens. The integration of correlative cryo-fluorescence microscopy, focused-ion beam milling, and micropatterning produces contextual three-dimensional architecture of cells. Montage tilt series may be processed in their entirety or as individual tiles suitable for sub-tomogram averaging, enabling efficient data processing and analysis.

biophysics↗

bioRxiv2020

Flagellar structures from the bacterium Caulobacter crescentus and implications for phage {Phi}CbK predation of multi-flagellin bacteria

Caulobacter crescentus is a gram-negative alpha-proteobacterium that commonly lives in oligotrophic fresh and salt-water environments. C. crescentus is a host to many bacteriophages, including {phi}CbK and {phi}CbK-like bacteriophages, which first adsorb to cells by interaction with the bacterial flagellum. It is commonly thought that the six paralogs of the flagellin gene present in C. crescentus are important for bacteriophage evasion. Here, we show that deletion of specific flagellins in C. crescentus can indeed attenuate {phi}CbK adsorption efficiency, although no single deletion completely ablates {phi}CbK adsorption. Thus, bacteriophage {phi}CbK likely recognizes a common motif amongst the six known flagellins in C. crescentus with varying degrees of efficiency. Interestingly, we observe that most deletion strains still generate flagellar filaments, with the exception of a strain that contains only the most divergent flagellin, FljJ, or a strain that contains only FljN and FljO. To visualize the surface residues that are likely recognized by {phi}CbK, we determined two high-resolution structures of the FljK filament, with and without an amino acid substitution that induces straightening of the filament. We observe post-translational modifications on conserved surface threonine residues of FljK that are likely O-linked glycans. The possibility of interplay between these modifications and {phi}CbK adsorption is discussed. We also determined the structure of a filament composed of a heterogeneous mixture of FljK and FljL, the final resolution of which was limited to approximately 4.6 [A]. Altogether, this work builds a platform for future investigation of how phage {phi}CbK infects C. crescentus at the molecular level.

microbiology↗