Biology subjects

Hill, C. H.

Publications and source records attributed to Hill, C. H..

8 recordsLinked to original sources

bioRxiv2026

Histone H3 availability is more important for development than H3.2 versus H3.3 subtype identity

The distinct contributions of replication-dependent and replication-independent histones to development and genome function remain unclear. In this study, we investigate how the distinct protein identities of the histone H3.2 and H3.3 subtypes contribute to development and gene regulation in Drosophila. Comparing animals in which the replication-independent H3.3 genes were mutated to produce the replication-dependent H3.2 protein with those carrying deletions of the replication-independent H3.3 genes revealed that replication-independent H3.3 is essential for fertility, adult locomotor behavior, and normal longevity. However, development to adulthood does not depend on which replication-independent H3 subtype is expressed from the H3.3 loci. Moreover, replication-independent H3.3 is not required to establish or maintain global patterns of chromatin accessibility or gene expression in the adult brain. Surprisingly, we find that expression of H3.2 from the replication-dependent HisC locus is essential in post-replicative cells in the absence of replication-independent H3.3, and we uncover a critical role for the HIRA histone chaperone complex in preserving genome function when replication-independent H3.3 is deleted. We conclude that an available pool of H3 is more critical than the specific identity of H3 in the pool.

genetics↗

bioRxiv2025

Structural and mechanistic insights into translation initiation on the enterovirus Type 1 IRES

Enteroviruses are a diverse group of pathogens that cause over one billion human infections annually. Upon cell entry, translation of the viral genome is directed by an internal ribosome entry site (IRES) within the 5' untranslated region. Despite early identification of the Type 1 poliovirus IRES, the structural and mechanistic basis for its activity remains poorly understood due to its size, flexibility and dependence on multiple host cell factors. Here, we reconstitute human translation initiation on a model poliovirus IRES and examine 48S complexes by cryo-electron microscopy. Our structures reveal how IRES domain IVc contacts ribosomal proteins uS19 and uS13, whilst a conserved GNRA tetraloop engages with the initiator tRNA during start-codon recognition. Disruption of these interfaces impairs IRES-dependent translation and viral replication. Together, our results provide new structural and mechanistic insights into initiation on the Type 1 IRES and reveal conserved RNA-RNA interactions critical for enterovirus translation.

molecular biology↗

bioRxiv2025

A DNA scaffold approach facilitates 5' labelling of the SARS-CoV-2 RNA pseudoknot for smFRET investigation

Single-molecule Forster resonance energy transfer (smFRET) studies of highly structured RNA molecules are often frustrated by issues with efficient dye conjugation. Here, we develop a DNA scaffold-based labelling strategy, and apply it to the frameshift-stimulating RNA pseudoknot from the SARS-CoV-2 genome. We prepare FRET-active reporters containing both Cy3 (donor) and Cy5 (acceptor) molecules and conduct measurements on freely diffusing single molecules, enabling the evaluation of conformational heterogeneity via smFRET population distributions. We identify that freely diffusing pseudoknots, modified at the base of stem 1, display a broad range of NaCl-dependent FRET states in solution, consistent with conformational freedom that extends beyond the static X-ray and cryo-EM structures. This work is a proof-of-principle demonstration of the feasibility of our DNA scaffold approach in enabling smFRET studies on this important class of biomolecule. Together, this work outlines new biochemical and biophysical approaches towards the study of RNA conformational dynamics in pseudoknots, riboswitches and other structured RNA elements.

biophysics↗

bioRxiv2025

A new protein-dependent riboswitch activates ribosomal frameshifting

Programmed -1 ribosomal frameshifting (PRF) is a translational control mechanism used by RNA viruses to regulate the relative abundance of proteins encoded in different reading frames. Cardioviruses exhibit the highest known PRF efficiency, with ~85% of ribosomes shifting into the -1 frame. This unusual event requires an interaction between the viral 2A protein and a stimulatory element in the RNA genome, but the basis for protein-dependence is unclear. To address this, here we investigate structure and dynamics of the PRF signal in Theiler's murine encephalitis virus (TMEV). By combining X-ray crystallography, small angle X-ray scattering (SAXS) and single-molecule fluorescence resonance energy transfer (smFRET), we show that 2A binding switches the RNA from a stem-loop conformation into a pseudoknot, and we demonstrate that pseudoknot formation is essential for efficient PRF in vitro and in cells. Together, these findings illustrate how the cardiovirus PRF element behaves as a protein-dependent riboswitch, defining the molecular mechanism by which frameshifting is conditionally activated.

molecular biology↗

bioRxiv2022

Structure of dormant bacterial ribosomes reveals an elusive translation factor with evolutionary connections to eukaryotic protein synthesis factors

During starvation and stress, virtually all organisms arrest protein synthesis to conserve energy. Inactive ribosomes are converted into a dormant state, in which they are protected from damage by hibernation factor proteins. In bacteria, two major families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats, and environmental stressors has confounded their discovery. In this study, using proteomics and cryo-EM, we identify a new dormancy factor from the psychrophilic bacterium Psychrobacter urativorans. By isolating ribosomes under cold-shock conditions, we observe a previously unknown protein bound to the ribosomal A site, protecting critical elements of both the decoding and peptidyl transferase centers. We show that this new factor, which we term Balon, is a homolog of the archaeo-eukaryotic translation factor aeRF1, providing a long-predicted evolutionary "missing link" between the eukaryotic and bacterial translation machinery. Our structures reveal that Balon is delivered to both vacant and actively translating ribosomes by EF-Tu, highlighting an unexpected and previously unknown role for this elongation factor in the bacterial stress response. We describe several unique structural motifs that allow Balon to bind ribosomes in an mRNA-independent manner, initiating a new mode of ribosome dormancy that can commence while ribosomes are still engaged in protein synthesis. Our bioinformatic analysis shows that putative Balon-encoding genes can be found within stress-response operons in nearly 20 % of all known bacterial species, including many human pathogens. Taken together, our work suggests that Balon/EF-Tu regulated ribosome dormancy is likely to be a ubiquitous stress-response mechanism throughout the bacterial kingdom. These findings call for a revision of our model of bacterial translation inferred from common model organisms and hold numerous implications for how we understand and study ribosome dormancy.

molecular biology↗

bioRxiv2020

Structural studies of Cardiovirus 2A protein reveal the molecular basis for RNA recognition and translational control

Programmed -1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein: a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to and stabilises the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we define the conformational repertoire of this element and measure changes in unfolding pathways arising from mutation and 2A binding. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, expand our understanding of the 2A-dependent gene expression switch and reveal how 2A accumulation may shut down translation during virus infection.

molecular biology↗

bioRxiv2020

Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler's murine encephalomyelitis virus

The 2A protein of Theilers murine encephalomyelitis virus (TMEV) acts as a switch to stimulate programmed -1 ribosomal frameshifting (PRF) during infection. Here we present the X-ray crystal structure of TMEV 2A and define how it recognises the stimulatory RNA element. We demonstrate a critical role for bases upstream of the originally predicted stem-loop, providing evidence for a pseudoknot-like conformation and suggesting that the recognition of this pseudoknot by beta-shell proteins is a conserved feature in cardioviruses. Through examination of PRF in TMEV-infected cells by ribosome profiling, we identify a series of ribosomal pauses around the site of PRF induced by the 2A-pseudoknot complex. Careful normalisation of ribosomal profiling data with a 2A knockout virus facilitated the identification, through disome analysis, of ribosome stacking at the TMEV frameshifting signal. These experiments provide unparalleled detail of the molecular mechanisms underpinning Theilovirus protein-stimulated frameshifting.

molecular biology↗

bioRxiv2017

The mechanism of sphingolipid processing revealed by a GALC-SapA complex structure

Sphingolipids are essential components of cellular membranes and defects in their synthesis or degradation cause severe human diseases. The efficient degradation of sphingolipids in the lysosome requires lipid-binding saposin proteins and hydrolytic enzymes. The glycosphingolipid galactocerebroside is the primary lipid component of the myelin sheath and is degraded by the hydrolase {beta}-galactocerebrosidase (GALC). This enzyme requires the saposin SapA for lipid processing and defects in either of these proteins causes a severe neurodegenerative disorder, Krabbe disease. Here we present the structure of a glycosphingolipid-processing complex, revealing how SapA and GALC form a heterotetramer with an open channel connecting the enzyme active site to the SapA hydrophobic cavity. This structure defines how a soluble hydrolase can cleave the polar glycosyl headgroups of these essential lipids from their hydrophobic ceramide tails. Furthermore, the molecular details of this interaction reveal how specificity of saposin binding to hydrolases is encoded.

molecular biology↗