Biology subjects

Weeks, K.

Publications and source records attributed to Weeks, K..

10 recordsLinked to original sources

bioRxiv2026

Microbial Growth in an Enceladus Ocean Analog Medium Informed by Mineral Stability Modeling

Evidence from the Cassini mission confirmed that Saturns moon Enceladus hosts a subsurface alkaline ocean where rock-water reactions may generate redox disequilibria capable of supporting microbial metabolisms. To investigate potential microbial survival under simulated Enceladus ocean conditions, we used thermodynamic modeling to develop a salt formulation consistent with one possible Enceladus ocean composition and supplemented it with putative microbial energy sources to create a growth medium. The medium was inoculated with samples from diverse ocean world analog environments on Earth to determine which microorganisms could persist under Enceladus-like conditions. The microorganisms persisting in this geochemically bounded medium were heterotrophic, metabolically versatile bacteria with low carbon requirements. Genomic and physiological analyses further showed the presence of multiple stress-response pathways, sodium-based bioenergetic systems, osmoregulation strategies, and other adaptations consistent with survival in alkaline, low-nutrient settings. These results suggest that some stress-tolerant heterotrophic bacteria may serve as useful model organisms for life in Enceladus subsurface ocean. These findings demonstrate the value of geochemically modeled media as a framework for constraining habitability, identifying relevant biosignatures, and probing potential microbial survival strategies beyond Earth.

microbiology↗

bioRxiv2026

RNA Structure Coordinates Translation Across the Meiotic Program

mRNA structure clearly modulates translation efficiency for individual transcripts, yet its role in coordinating translation across many transcripts remains poorly defined. Meiosis offers a compelling test case, involving large-scale gene expression changes coordinated across hundreds of mRNAs under conditions where transcription is constrained by chromosome condensation. We profiled mRNA structures across yeast meiosis, generating a high-resolution structurome encompassing ~70% of annotated mRNAs, including multi-time-point measurements for 2,084 transcripts. Transcripts upregulated during meiosis generally adopt flexible structures that enhance translation, whereas mRNAs with complex 5' UTR and coding-region structures show suppressed translation, indicating that RNA structure globally shapes meiotic translation. We further observed a high-low-high oscillation in cytoplasmic RNA helicase levels across meiosis. Together, these findings support a model in which RNA structure and helicase expression act jointly to program stage-specific translation of hundreds of mRNAs, with highly structured transcripts selectively translated at late stages. Consistent with this model, disrupting the structure of the abundant transcript CCW22, or altering Ded1p helicase levels, impaired meiotic progression in an RNA structure-dependent manner. Our study reveals that the concerted action of RNA structure and helicases coordinates cell-wide translation dynamics to meet stage-specific demands, especially critical when transcription is limited during meiotic divisions.

genomics↗

bioRxiv2025

fpocketR: A platform for identification and analysis of ligand-binding pockets in RNA

Small molecules that bind specific sites in RNAs hold promise for altering RNA function, manipulating gene expression, and expanding the scope of druggable targets beyond proteins. Identifying binding sites in RNA that can engage ligands with good physicochemical properties remains a significant challenge. fpocketR is a software and framework for identifying, characterizing, and visualizing ligand-binding sites in RNA. fpocketR was optimized, through a comprehensive analysis of currently available RNA-ligand complexes, to identify pockets in RNAs able to bind small molecules possessing favorable properties, generally termed drug-like. Here, we demonstrate multiple, complex, uses of fpocketR to analyze RNA-ligand interactions and novel pockets in small and large RNAs, to assess ensembles of RNA structure models, to identify pockets in dynamic RNA systems, and to evaluate the shapes of RNA pockets. fpocketR performs best with RNA structures visualized at atomistic resolution but also provides useful information with lower resolution structures and computational models. fpocketR is a powerful, ligand-agnostic tool for discovery and analysis of targetable pockets in RNA molecules.

bioinformatics↗

bioRxiv2024

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, it is hypothesized that these sites must be in proximity. Inverted repeat sequences, such as Alu elements, in the upstream and downstream introns are predicted to base-pair and represent one mechanism for inducing proximity. Here, we investigate the pre-mRNA structure of the human HIPK3 gene at exon 2, which forms a circular RNA via backsplicing. We leverage multiple chemical probing techniques, including the recently developed SHAPE- JuMP strategy, to characterize secondary and tertiary interactions in the pre- mRNA that govern backsplicing. Our data confirm that the antisense Alu elements, AluSz(-) and AluSq2(+) in the upstream and downstream introns, form a highly- paired interaction. Circularization requires formation of long-range Alu-mediated base pairs but does not require the full-length AluSq2(+). In addition to confirming long-range base pairs, our SHAPE-JuMP data identified multiple long-range interactions between non-pairing nucleotides. Genome-wide analysis of inverted repeats flanking circular RNAs confirm that their presence favors circularization, but the overall effect is modest. Together these results suggest that secondary structure considerations alone cannot fully explain backsplicing and additional interactions are key.

molecular biology↗

bioRxiv2023

Immune-induced remodelling of mRNA structurome regulates uORF-mediated translation

To survive stress, eukaryotes selectively translate stress-related transcripts while inhibiting growth-associated protein production. How this translational reprogramming occurs under biotic stress has not been systematically studied. To identify common features shared by transcripts with stress-upregulated translation efficiency (TE-up), we first performed high-resolution ribosome-sequencing in Arabidopsis during pattern-triggered immunity and found that TE-up transcripts are enriched with upstream open reading frames (uORFs). Under non-stress conditions, start codons of these uORFs (uAUGs) have higher-than-background ribosomal association. Upon immune induction, there is an overall downshift in ribosome occupancy at uAUGs, accompanied by enhanced translation of main ORFs (mORFs). Using in planta nucleotide-resolution mRNA structurome probing, we discovered that this stress-induced switch in translation is mediated by highly structured regions detected downstream of uAUGs in TE-up transcripts. Without stress, these structures are responsible for uORF-mediated inhibition of mORF translation by slowing progression of the translation preinitiation complex to initiate translation from uAUGs, instead of mAUGs. In response to immune induction, uORF-inhibition is alleviated by three Ded1p/DDX3X-homologous RNA helicases which unwind the RNA structures, allowing ribosomes to bypass the inhibitory uORFs and upregulate defence protein production. Conservation of the RNA helicases suggests that mRNA structurome remodelling is a general mechanism for stress-induced translation across kingdoms.

plant biology↗

bioRxiv2022

Maternal diet and gut microbiota influence predisposition to cardiovascular disease in the offspring

Cardiovascular disease is one of the most significant causes of death globally, especially in regions where unhealthy diets are prevalent and dietary fibre intake is low.1,2 Fibre, particularly prebiotic types that feed gut microbes, is essential for maintaining healthy gut microbial ecosystems.3 One assumption has been that cardiovascular health relates directly to lifestyle choices in adult life. Here, we show in mice that some of these benefits operate from the prenatal stage and relate to the diet and gut microbiome of the mother. Intake of fibre during pregnancy shaped the mothers gut microbiome, which had a lasting founding effect on the offsprings microbial composition and function. Maternal fibre intake during pregnancy significantly changed the cardiac cellular and molecular landscape in the offspring, protecting them against the development of cardiac hypertrophy, remodelling, and inflammation. These suggest a role for foetal exposure to maternal-derived gut microbial metabolites, which are known to cross the placenta and drive epigenetic changes. Maternal fibre intake led to foetal epigenetic reprogramming of the atrial natriuretic peptide gene (Nppa), protective against heart failure. These results underscore the importance of dietary intake and the gut microbiome of the mother during pregnancy for cardiovascular disease in the offspring.

microbiology↗

bioRxiv2021

Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures

Betacoronavirus SARS-CoV-2 infections caused the global Covid-19 pandemic. The nucleocapsid protein (N-protein) is required for multiple steps in the betacoronavirus replication cycle. SARS-CoV-2-N-protein is known to undergo liquid-liquid phase separation (LLPS) with specific RNAs at particular temperatures to form condensates. We show that N-protein recognizes at least two separate and distinct RNA motifs, both of which require double-stranded RNA (dsRNA) for LLPS. These motifs are separately recognized by N-proteins two RNA binding domains (RBDs). Addition of dsRNA accelerates and modifies N-protein LLPS in vitro and in cells and controls the temperature condensates form. The abundance of dsRNA tunes N-protein-mediated translational repression and may confer a switch from translation to genome packaging. Thus, N-proteins two RBDs interact with separate dsRNA motifs, and these interactions impart distinct droplet properties that can support multiple viral functions. These experiments demonstrate a paradigm of how RNA structure can control the properties of biomolecular condensates.

molecular biology↗

bioRxiv2020

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate

A mechanistic understanding of the SARS-CoV-2 viral replication cycle is essential to develop new therapies for the COVID-19 global health crisis. In this study, we show that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with the viral genome, and propose a model of viral packaging through LLPS. N-protein condenses with specific RNA sequences in the first 1000 nts (5-End) under physiological conditions and is enhanced at human upper airway temperatures. N-protein condensates exclude non-packaged RNA sequences. We comprehensively map sites bound by N-protein in the 5-End and find preferences for single-stranded RNA flanked by stable structured elements. Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules thus presenting screenable processes for identifying antiviral compounds effective against SARS-CoV-2.

biochemistry↗

bioRxiv2020

Time-resolved, single-molecule, correlated chemical probing of RNA

Methods for capturing the folding dynamics of functionally important RNAs, especially large RNAs, have relied primarily on global measurements of structure or on per-nucleotide chemical probing. These approaches infer, but do not directly measure, through-space tertiary interactions. Here we introduce trimethyloxonium (TMO) as a chemical probe for RNA. TMO enables time-resolved, single-molecule, through-space structure probing of RNA folding using a correlated chemical probing framework. TMO methylates RNA about 90 times faster than the widely used dimethyl sulfate probe, allowing structure interrogation on the second time scale. We used TMO to monitor folding of the RNase P RNA - a functional RNA with extensive long-range and noncanonical interactions - by direct measurement of through-space tertiary interactions in a time-resolved way. Time-dependent correlation changes directly revealed the central role of a long-range tertiary loop-loop interaction that guides native RNA folding. Single-molecule, time-resolved RNA structure probing with TMO is poised to reveal a wide range of dynamic RNA folding processes and principles of RNA folding.

biochemistry↗

bioRxiv2017

Zoonotic Babesia microti in the northeastern U.S.: evidence for the expansion of a specific parasite lineage

The recent range expansion of human babesiosis in the northeastern United States, once found only in restricted coastal sites, is not well understood. This study sought to utilize a large number of samples to examine the population structure of the parasites on a fine scale to provide insights into the mode of emergence across the region. 228 B. microti samples collected in endemic northeastern U.S. sites were genotyped using published VNTR markers. The genetic diversity and population structure were analysed on a geographic scale using Phyloviz and TESS. Three distinct populations were detected in northeastern US, each dominated by a single ancestral type. In contrast to the limited range of the Nantucket and Cape Cod populations, the mainland population dominated from New Jersey eastward to Boston. Ancestral populations of B. microti were sufficiently isolated to differentiate into distinct populations. Despite this, a single population was detected across a large geographic area of the northeast that historically had at least 3 distinct foci of transmission, central New Jersey, Long Island and southeastern Connecticut. We conclude that a single B. microti genotype has expanded across the northeastern U.S. The biological attributes associated with this parasite genotype that have contributed to such a selective sweep remain to be identified.\n\nAuthor summaryBabesiosis is a disease caused by a protozoan parasite, Babesia microti, related to malaria. The disease is acquired by the bite of the deer tick, the same tick that transmits Lyme disease. Although Lyme disease rapidly emerged over a wide range within the last 40 years, babesiosis remained rare with an extremely focal distribution. Within the last decade, the number of reports of babesiosis cases has increased from an expanded area of risk, particularly across the mainland of southern New England. We determined whether the expanded risk may be due to local intensification of transmission as opposed to introduction of the parasite. Historical fragmentation of the landscape suggests that sites of B. microti transmission should have been isolated and thus evidence of multiple genetically distinct populations should be found. By a genetic fingerprinting method, we found that samples from the new mainland sites were all genetically similar. We conclude that one parasite genetic lineage has recently expanded its distribution and now dominates, suggesting that it has some phenotypic attribute that may confer a selective advantage over others.

epidemiology↗