Biology subjects

Howells, G.

Publications and source records attributed to Howells, G..

4 recordsLinked to original sources

bioRxiv2026

Paired in situ and molecular analyses identify mechanisms of pathogen persistence within environmental communities

Natural environments are a key reservoir for many opportunistic pathogens, yet mechanisms enabling persistence within complex microbial communities remain poorly defined. Current methods do not adequately link molecular and functional understanding of bacterial persistence to the activities of bacteria within their natural microbial community. Here we combine in situ culture-independent techniques, including metagenomics and metatranscriptomics, with isolate-level functional genomics and mutant studies to understand how opportunistic pathogens from the genera Escherichia, Klebsiella, and Enterococcus survive in urban-adjacent freshwater ecosystems. . Our results show that potential pathogens from each of these genera are both present and active within freshwater microbial communities. We further investigate a mouse-virulent isolate of the E. coli UPEC lineage ST73 isolated directly from this ecosystem, showing that this isolate persists in freshwater microcosms for at least one month. Paired transcriptomics and genome-scale fitness screening in creek water containing autochthonous microbiota identified E. coli genes required for persistence, including those involved in amino acid metabolism, nucleotide biosynthesis and biogenesis of curli. Isolate-resolved metatranscriptomics analysis supported these findings by revealing that many of these genes were highly expressed in situ. Deletion of curli structural genes resulted in reduced biofilm formation and a fitness defect specifically in the presence of freshwater microbiota, indicating that these structures promote environmental survival by improving E. coli competitiveness. Our study deepens our understanding of E. coli survival in waterways, while providing a broadly applicable framework for interrogating mechanisms of pathogen persistence in complex environments and communities.

microbiology↗

bioRxiv2024

ProEnd: A Comprehensive Database for Identifying HbYX Motif-Containing Proteins Across the Tree of Life

The proteasome plays a crucial role in cellular homeostasis by degrading misfolded, damaged, or unnecessary proteins. Understanding the regulatory mechanisms of proteasome activity is vital, particularly the interaction with activators containing the hydrophobic-tyrosine-any amino acid (HbYX) motif. Here, we present ProEnd, a comprehensive database designed to identify and catalog HbYX motif-containing proteins across the tree of life. Using a simple bioinformatics pipeline, we analyzed approximately 73 million proteins from 22,000 reference proteomes in the UniProt/SwissProt database. Our findings reveal the widespread presence of HbYX motifs in diverse organisms, highlighting their evolutionary conservation and functional significance. Notably, we observed an interesting prevalence of these motifs in viral proteomes, suggesting strategic interactions with the host proteasome. As validation two novel HbYX proteins found in this database were tested and found to directly interact with the proteasome. ProEnds extensive dataset and user-friendly interface enable researchers to explore the potential proteasomal regulator landscape, generating new hypotheses to advance proteasome biology. This resource is set to facilitate the discovery of novel therapeutic targets, enhancing our approach to treating diseases such as neurodegenerative disorders and cancer. Link: http://proend.org/

cell biology↗

bioRxiv2024

Proteasome hyperactivation rewires the proteome enhancing stress resistance, proteostasis, lipid metabolism and ERAD in C. elegans.

Age-related proteinopathies, including Alzheimers and Parkinsons disease, are driven by the toxic accumulation of misfolded proteins, particularly intrinsically disordered proteins (IDPs), that overwhelm cellular proteostasis. The proteasome is responsible for the clearance of these proteins, but it is unclear why it fails to do so in these diseases. Here, we report a novel strategy employing a C. elegans model with a hyperactive 20S proteasome (3{Delta}N) to achieve selective activation. This activation robustly enhances the degradation of IDPs and misfolded proteins, markedly reduces oxidative damage, and significantly improves ER-associated degradation (ERAD). Notably, aggregation-prone substrates, such as endogenous vitellogenins and human alpha-1 antitrypsin (ATZ), are efficiently cleared. Proteomic and transcriptomic reprogramming reveals systemic adaptations characterized by increased protein turnover and enhanced oxidative stress resistance, independent of superoxide dismutases. Strikingly, proteasome hyperactivation extends lifespan and enhances stress resistance independently of known proteostasis pathways including the canonical unfolded protein response mediated by xbp-1. Our findings provide substantial support for a "20S pathway" of proteostasis that alleviates protein aggregation and oxidative stress, offering a promising therapeutic strategy for neurodegenerative diseases TeaserEnhanced disordered protein clearance by the 20S proteasome in worms prevents toxic protein buildup and promotes stress resistance and longevity.

cell biology↗

bioRxiv2021

Conformational Change of Syntaxin-3b in Regulating SNARE Complex Assembly in the Ribbon Synapses

Neurotransmitter release of synaptic vesicles relies on the assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, consisting of syntaxin and SNAP-25 on the plasma membrane and synaptobrevin on the synaptic vesicle. The formation of the SNARE complex progressively zippers towards the membranes, which drives membrane fusion between the plasma membrane and the synaptic vesicle. However, the underlying molecular mechanism of SNARE complex regulation is unclear. In this study, we investigate the syntaxin-3b isoform found in the retinal ribbon synapses using single-molecule fluorescence resonance energy transfer (smFRET) to monitor the conformational changes of syntaxin-3b that modulate the SNARE complex formation. We found that syntaxin-3b is predominantly in a self-inhibiting closed conformation, inefficiently forming the ternary SNARE complex. Conversely, a phosphomimetic mutation (T14E) at the N-terminal region of syntaxin-3b promoted the open conformation, similar to the constitutively open form of syntaxin LE mutant. When syntaxin-3b is bound to Munc18-1, SNARE complex formation is almost completely blocked. Surprisingly, the T14E mutation of syntaxin-3b partially abolishes Munc18-1 regulation, acting as a conformational switch to trigger SNARE complex assembly. Thus, we suggest a model where the conformational change of syntaxin-3b induced by phosphorylation initiates the release of neurotransmitters in the ribbon synapses.

neuroscience↗