Biology subjects

Sweeney, T.

Publications and source records attributed to Sweeney, T..

4 recordsLinked to original sources

bioRxiv2026

The Structure of the Picornaviral 2C:RNA holoenzyme: Molecular Basis of RNA binding and specificity by a AAA+ protein

Picornaviruses are one of the leading agents of animal and human infectious disease with at least 8 billion infections a year and cause a range of symptoms including respiratory failure and acute flaccid myelitis1. The most conserved nonstructural protein in picornaviruses is 2C2, a member of the AAA+ family of ATPases that binds RNA, and a broad spectrum antiviral target3-5. Despite its crucial role in the viral life cycle and as a clinical target, no structure of 2C bound to RNA has been structurally determined. Here we present the first structure of 2C as a hexamer bound to single stranded RNA in its central pore; a novel AAA+ protein:substrate interaction. Using the 2C:RNA holoenzyme complex structure, we characterize the mode that this AAA+ protein employs to specifically bind single stranded RNA, and demonstrate that mutations to key residues inhibit both RNA binding and viral replication in Apthovirus and Enterovirus systems, and show that the core residues responsible for binding are broadly conserved in viruses beyond Picornaviridae. Finally, we reveal that the 2C:RNA holoenzyme complex is conformationally more similar to a protein translocase adapted to bind RNA rather than other viral DNA binding SF3 helicases, underscoring how the AAA+ core module can be adapted for a variety of biochemical substrates.

biophysics↗

bioRxiv2022

Maternal and/or direct supplementation with a combination of a casein hydrolysate and yeast β-glucan on post-weaning performance and intestinal health in the pig

A 2 x 2 factorial experiment was conducted to investigate the effect of maternal supplementation from day 83 of gestation and/or direct supplementation from weaning of a bovine casein hydrolysate plus a yeast {beta}-glucan (CH-YBG) on pig performance and intestinal health on day ten post-weaning. Twenty cross bred gilts (Large White x Landrace) were randomly assigned to one of two dietary groups (n = 10 gilts/group): basal diet (basal sows) and basal diet supplemented with CH-YBG (supplemented sows) from day 83 of gestation until weaning (2g/sow/day). At weaning, 120 pigs (6 pigs/sow) were selected. The two dam groups were further divided, resulting in four experimental groups (10 replicates/group; 3 pigs/pen) as follows: 1) BB (basal sows + basal pigs); 2) BS (basal sows + supplemented pigs); 3) SB (supplemented sows + basal pigs); 4) SS (supplemented sows + supplemented pigs). Supplemented pigs were offered 0.5g CH-YBG/kg of feed for 10 days post-weaning. On day 10 post-weaning, 1 pig/pen was humanely sacrificed and samples were taken from the gastrointestinal tract for analysis. Pigs weaned from supplemented sows (SS, SB) had reduced faecal scores and incidence of diarrhoea (P<0.05) compared to pigs weaned from basal sows (BB, BS), with SS pigs not displaying the transient rise in faecal scores seen in the other three groups from day 3 to day 10 post-weaning (P<0.05). Pigs weaned from supplemented sows had reduced feed intake (P<0.05), improved feed efficiency (P<0.05), increased butyrate concentrations (P<0.05), increased abundance of Lactobacillus (P<0.05) and decreased abundance of Enterobacteriaceae and Campylobacteraceae (P<0.05) compared to pigs weaned from basal sows. In conclusion, a combination of both maternal and direct supplementation with CH-YBG is the desirable feeding strategy to ameliorate the post-weaning challenge in pig production systems.

developmental biology↗

bioRxiv2021

Distinct stress-dependent signatures of cellular and extracellular tRNA-derived small RNAs (tDRs)

The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may yield novel biomarkers for different diseases, and potentially identify key signaling pathways important for disease progression. tRNAs and tRNA-derived small RNAs (tDRs) comprise one of the most abundant RNA species in cells and have been associated with cellular stress responses. The presence of RNA modifications on tDRs has been an obstacle for accurately identifying tDRs with conventional small RNA sequencing. Here, we use AlkB-facilitated methylation sequencing (ARM-seq) to uncover a comprehensive landscape of cellular and extracellular tDR expression in a variety of human and rat cells during common stress responses, including nutritional deprivation, hypoxia, and oxidative stress. We found that extracellular tDRs have a distinct fragmentation signature with a predominant length of 31-33 nts and a highly specific termination position when compared with intracellular tDRs. Importantly, we found these signatures are better discriminators of different cellular stress responses compared to extracellular miRNAs. Distinct extracellular tDR signatures for each profiled stressor are elucidated in four different types of cells. This distinct extracellular tDR fragmentation pattern is also noted in plasma extracellular RNAs from patients on cardiopulmonary bypass. The observed overlap of these patient tDR signatures with the signatures of nutritional deprivation and oxidative stress in our cellular models provides preliminary in vivo corroboration of our findings and demonstrates the potential to establish novel extracellular tDR biomarkers in human disease models.

cell biology↗

bioRxiv2019

Flaviviruses exploit fine-tuning of the interferon response to promote replication

The establishment of a virus infection is the result of the pathogens ability to replicate in a hostile environment generated by the hosts immune system. Here, we found that ISG15 restricts Dengue and Zika viruses replication through the stabilisation of its binding partner USP18. ISG15 expression was necessary to control DV replication driven by both autocrine and paracrine type one interferon (IFN-I) signalling. Moreover, USP18 competes with NS5-mediated STAT2 degradation, a major mechanism for establishment of flavivirus infection. Strikingly, reconstitution of USP18 in ISG15-deficient cells was sufficient to restore the STAT2s stability and restrict virus growth, suggesting that the IFNAR-mediated ISG15 activity is also antiviral. Our results add a novel layer of complexity in the virus/host interaction interface and suggest that NS5 has a narrow window of opportunity to degrade STAT2, therefore suppressing hosts IFN-I mediated response and promoting virus replication. IMPORTANCEDisease is an emergent property that results from a microorganisms ability to replicate in a given host and the latters immune response. Here we describe how the immunoregulatory function of ISG15 (an interferon stimulated gene) affects Dengue and Zika virus replication by occupying a niche used by the virus non-structural protein 5 (NS5) to evade hosts immunity. In the absence of ISG15, NS5 efficiently degrades a main signalling hub of innate immunity (STAT2), leading to cell immune suppression and consequently virus growth. This sheds light into how flaviviruses intimately interact with the host immune system and could lead to a host-based therapy target.

immunology↗