Biology subjects

Lyons, S. M.

Publications and source records attributed to Lyons, S. M..

15 recordsLinked to original sources

bioRxiv2026

Overwinter roost activity patterns in response to environmental conditions along a rural-urban gradient

1. Organisms rely on environmental cues, such as moonlight illumination and weather, to modulate nocturnal behaviors that reduce predation risk and conserve energy during demanding periods. Urbanization can alter the reliability of cues, potentially impairing organisms' ability to respond appropriately with consequences in increasingly urbanized landscapes. 2. We leveraged the Motus Wildlife Tracking System to identify roost initiation, roost departure and nocturnal restlessness of dark-eyed juncos (Junco hyemalis) overwintering along an urban to rural gradient to determine if activity patterns are affected by weather, moonlight illumination, and urbanization. 3. Nocturnal behavior of overwintering juncos varied with environmental factors, including moonlight illumination and temperature. However, the strength of these responses differed among sites, suggesting that natural cues of moonlight illumination were masked in urban areas, where individuals were more responsive to temperature. 4. Our results suggest that urbanization weakens birds' responsiveness to natural light cues, likely because artificial lighting reduces the visibility of moonlight; representing a key mechanism by which human-altered landscapes can disrupt nocturnal ecology in birds.

animal behavior and cognition↗

bioRxiv2026

roostR: An R package to examine diel activity patterns from Motus radio telemetry data

1. Monitoring the diel activity patterns of free-living animals is a methodological challenge. Signal strength fluctuations from Very High Frequency (VHF) radio transmitters deployed within the Motus Wildlife Tracking System can be used as a proxy for activity. However, analytical tools to extract behavioral metrics that quantify activity patterns from these data are needed. 2. We developed roostR, an open-source R package that converts Motus detection data into quantitative behavioral metrics, including roost initiation and departure, roost duration, observation time, and restlessness. The package uses a sequential pipeline built around signal volatility and rolling medians to detect transitions between active and inactive states. Default parameter values were tuned using data from 55 dark-eyed juncos (Junco hyemalis) overwintering in southeastern Ohio. 3. We provide an example from a dark-eyed junco over a 58-day period. roostR estimated roost onset on 48 nights and departure on 56 mornings, with higher rolling median signal differences during the day than at night, consistent with a diurnal animal, and variable restlessness periods each night. We also used the package to estimate roost behavior of an American tree sparrow (Spizelloides arborea) over 43-nights. 4. roostR enables researchers to extract individual activity data from Motus datasets. Because all thresholds are user-adjustable, the pipeline is adaptable across species, tag specifications, and ecological contexts, enabling researchers to test hypotheses about how environmental factors influence diel activity patterns.

animal behavior and cognition↗

bioRxiv2026

eIF4E3 drives translation of viral mRNAs with short 5' UTRs

Eukaryotic cells express three paralogs of the cap-binding protein eIF4E, yet the functions of the less-studied family members remain poorly understood. Here we demonstrate that eIF4E3, a paralog whose expression is tissue-restricted and whose activity is insensitive to inhibition by eIF4E-binding proteins (4EBPs), drives efficient translation of viral mRNAs with short 5 untranslated regions (UTRs). Many negative-strand RNA viruses (NSVs), including vesicular stomatitis virus (VSV), respiratory syncytial virus (RSV), and influenza A virus (IAV), produce mRNAs with extremely short 5UTRs that are incompatible with canonical cap-dependent scanning translation initiation. Using an auxin-inducible degron (AID) system to acutely deplete endogenous eukaryotic initiation factors during active viral infection, we demonstrate that translation of these short-UTR viral mRNAs occurs independently of eIF4E1, the canonical cap-binding protein, while remaining dependent on eIF4E3. In contrast, Ebola virus (EBOV), whose mRNAs bear long, structured 5UTRs, remains eIF4E1-dependent, implicating 5UTR length and structural complexity as cis determinants of eIF4E paralog selectivity. During VSV infection, 4EBP dephosphorylation sequesters eIF4E1 and broadly suppresses host cap-dependent translation. Because eIF4E3 escapes 4EBP-mediated regulation and preferentially engages short, unstructured 5UTRs, it is uniquely positioned to sustain viral protein synthesis under these conditions. These findings reveal that VSV exploits a cellular paralog-switching mechanism by co-opting eIF4E3 to maintain viral translation when canonical eIF4F activity is suppressed and establish eIF4E3 as a proviral factor whose tissue-restricted expression in the lung may influence susceptibility to clinically important respiratory pathogens.

molecular biology↗

bioRxiv2026

The enteroviral protease target LSM14A operates outside of P-bodies to augment antiviral innate immunity

Antiviral innate immune networks in human cells comprise core components that serve as central signaling hubs and several context-dependent modulators whose role may be virus- or tissue-specific. One such modulator is LSM14A, which potentiates innate immune response but is not essential. We recently showed that enteroviruses deploy their protease activity to cleave LSM14A, thereby disabling its antiviral function. In this study, we probe the molecular mechanism by which LSM14A contributes to innate immunity. We show that although LSM14A predominantly localizes to processing bodies (P-bodies; PBs), this localization is not essential for its innate immune function. Likewise, association with peroxisomes does not contribute to its immune activity. Instead, an unbiased systems-level interactomic analysis reveals a distinct cohort of LSM14A-associated proteins that assemble outside canonical PBs and peroxisomes following infection with Sendai virus, a robust inducer of innate immunity. Functional interrogation of these interactors demonstrate that several are essential for LSM14A-dependent amplification of antiviral signaling. Together, these findings uncover a functional axis of LSM14A that operates independently of its canonical subcellular localizations and is mediated through a specialized interaction network, improving our understanding of how this protein reinforces the antiviral innate immune system.

microbiology↗

bioRxiv2026

Proteolytic dissection of eIF4G reveals the closed-loop mRNP as an architecture for translation repression.

Formation of a "closed-loop" mRNP, in which the 5' cap and 3' poly(A) tail are bridged by eIF4E-eIF4G-PABP interactions, has long been proposed to drive efficient translation initiation. Direct tests of this model in mammalian cells have remained elusive. Using auxin-inducible degron (AID) technology to acutely deplete eIF4G1, we find that global translation is only partially reduced and recovers without restoration of eIF4G1 levels. We identify eIF4G3 as an underappreciated contributor to basal translation that buffers translational output upon eIF4G1 loss without increased protein expression, explaining the modest defects observed in prior RNAi-based studies. Systematic replacement of eIF4G1 with defined cleavage products and interaction mutants reveals that PABP binding by eIF4G1 is dispensable for bulk translation initiation: the central caspase-3 cleavage fragment of eIF4G1 (casp3-cpM), which lacks the PABP-interaction domain, fully rescues global protein synthesis, and acute depletion of both major cytoplasmic PABP paralogs primarily destabilizes mRNAs rather than impairing initiation. In contrast, the N-terminal enteroviral 2A cleavage product (2A-cpN) is a potent, dominant translational repressor that requires simultaneous eIF4E and PABP engagement to form a dead-end closed-loop mRNP that sequesters initiation factors without enabling 43S recruitment. These findings reveal that the eIF4G-PABP closed-loop architecture is not required for productive initiation but can be actively co-opted for translational silencing. This explains why viral eIF4G cleavage, but not factor depletion, produces near-complete translational shutoff. The modular architecture of eIF4G enables diametrically opposing translational outcomes through selective proteolytic processing.

molecular biology↗

bioRxiv2026

Decreased tRNA abundance contributes to decreased translation elongation rate in a prolonged mitosis

Cells undergo dramatic structural rearrangements upon entering mitosis. In addition, the biochemistry of mitotic cells is dramatically altered, including a significant decrease in protein synthesis. The majority of studies of mitotic translation have used cells synchronized by cell cycle altering drugs in transformed cells and much less is known about mitotic translation in primary cells under native conditions. Previous work has found that mitosis activates the integrated stress response (ISR) to trigger eIF2 phosphorylation, but little is known about the input for this response. In this study, we focus on mitotic translational regulation in an immortalized, non-transformed cell line. We confirm decreased mitotic protein synthesis in primary cells and under native conditions. Additionally, we confirm activation of the ISR by phosphorylation of eIF2 during both normal and prolonged mitosis. Interestingly, we also find that decreased translational elongation during mitosis, as evidenced by increased eEF2 phosphorylation and a slower elongation rate. Analysis of mitotic ribosome profiling data revealed an increase in pausing at Alanine-GCG codons during mitosis and a decreased abundance of its cognate tRNA-AlaCGC by northern blotting. Decreased tRNA-AlaCGC is likely sustained by the inability to synthesize additional tRNA due to RNAPol III inhibition in mitosis, yielding an stronger effect with an increased time in mitosis. These results suggest that decreased translation elongation in mitosis triggers inhibition of initiation to decrease global protein synthesis.

cell biology↗

bioRxiv2025

Metal stress uncouples early pre-rRNA processing from ISR activation and reveals flexible checkpoints in human ribosome biogenesis

Ribosome synthesis is one of the most energy-intensive processes in a growing cell, consuming more than 60% of cellular energy reserves. As such, ribosome biogenesis is highly sensitive to stress to prevent costly expenditures under adverse conditions. Moreover, successful assembly requires precise stoichiometric balance between ribosomal proteins and ribosomal RNAs. Here, we define novel regulatory mechanisms of ribosome biogenesis under stress that reveal previously unrecognized aspects of rRNA maturation. We demonstrate that early pre-rRNA processing is particularly sensitive to stress induced by environmentally relevant heavy metals. Surprisingly, our analysis shows that 5' and 3' end processing can be uncoupled in human cells, with 3' end cleavage occurring independently of 5' end processing. We further show that classical inducers of endoplasmic reticulum stress suppress ribosomal protein synthesis without inhibiting rRNA transcription, leading to an imbalance between these essential components of ribosome assembly. This imbalance may exacerbate cellular stress and compromise proteostasis. Together, our findings uncover stress-specific checkpoints in ribosome biogenesis that link environmental exposures to disrupted nucleolar function and highlight new layers of regulation in human rRNA maturation.

biochemistry↗

bioRxiv2024

G-quadruplex topologies determine the functional outcome of guanine-rich bioactive oligonucleotides

Guanine-rich nucleic acid sequences can exert sequence and/or structure specific activities to influence biological and pathobiological cellular processes. As such, it has been reported that different G-rich oligonucleotides (both DNA and RNA) can have cytotoxic as well as cytoprotective effects to the cells. However, the mechanisms of such a biological outcome are unclear. In this report, we report that G-rich DNA oligonucleotides (ODNs) that can form four stranded secondary structures called G-quadruplexes (G4s) can have topology-dependent biological outcome. Using different biochemical, biophysical, and cellular approaches, we demonstrate that only the parallel topology G4-forming ODNs can repress eukaryotic translation by directly interacting with eukaryotic translation initiation protein 1 (EIF4G1), while the antiparallel topology G4s do not have inhibitory effect on mRNA translation To the best of our knowledge, this is the first report to directly connect the G4 topological differences with differential functional biological impacts. Our study provides the foundation for the rational design of G-rich oligonucleotides for a desired therapeutic outcome.

biochemistry↗

bioRxiv2024

Repurposing tRNA isodecoders for non-canonical functions via tRNA cleavage

Transfer RNAs (tRNAs) are the key adaptor molecules aiding protein synthesis. Hundreds of tRNA genes are found in the human genome but the biological significance of this genetic excess is still enigmatic. The tRNA repertoires are variable between tissues and cells as well as during development. Such variations can only be partially explained by the correlation to the physiological needs in protein production, e.g. by changes in the expression of tRNA isoacceptor sets (tRNAs charged with the same amino acid but bearing different anticodons). However, changes in the expression levels of individual isodecoders (tRNAs with the same anticodon) are less understood. Besides canonical functions in mRNA translation, tRNAs are implicated in non-canonical functions unrelated to protein synthesis. tRNAs are rich source of small non-protein coding RNAs called tRNA-derived RNAs (tDRs), which include tRNA-derived stress-induced RNAs (tiRNAs) formed in response to stress. Here, we show that tiRNAs derived from isodecoders different in a single nucleotide can also differ in their activities. Specifically, we show that isodecoder sets for tRNAHis-GTG, tRNAGly-GCC and tRNACys-GCA are cleaved by ribonucleases to yield 5-tiRNAs showing differential activity towards mRNA reporter translation. Our data propose a model where cleavage repurposes specific tRNA isodecoders for non-canonical functions. Significance StatementThe human genome encodes hundreds of transfer RNA (tRNA) genes to decode 61 codons. The basis for such genetic redundancy is unclear but the increase in the number of tRNA genes goes in concert with the complexity of an organism. While changes in the expression of isoacceptor tRNA pools can reflect adaptation to demanding protein synthesis needs and/or codon usage, the variations in the expression of the individual tRNA isodecoders are documented but poorly understood. Such expression variations are hypothesized to contribute to non-canonical tRNA functions, yet physiological relevance remains ambiguous. We report here that specific tRNA isodecoders can be functionally repurposed through cleavage that produces tRNA-derived RNAs (tDRs). The repurposing employs nucleotide variations in isodecoders leading to the production of distinct sets of tDRs with variable bioactivities.

molecular biology↗

bioRxiv2022

Cytoplasmic processing of human transfer RNAs

Biogenesis of different classes of eukaryotic RNAs proceeds via different pathways that require strict spatiotemporal resolution. The intracellular organization has evolved to provide order for RNA processing to coordinate different maturation steps with specific enzymatic reaction. In higher eukaryotes, processing of transfer RNAs (tRNAs) is postulated to be almost entirely intranuclear, while in lower eukaryotes like yeast, tRNA maturation is both nuclear and cytoplasmic. Here, we show that tRNA processing is largely cytosolic event in human cells. After transcription, unprocessed precursors of tRNAs (pre-tRNAs) bound by La protein are exported from the nucleus into the cytoplasm. Using cell fractionation analysis and pre-tRNA-specific fluorescence in situ hybridization (FISH) protocol, we show tRNA splicing/ligation and end-processing takes place in the cytoplasm where majority of processing enzymes is also located. We propose here a model where processing of intron-less and intron-containing pre-tRNAs is cytoplasmic similarly to the observed in lower eukaryotes, although tRNA splicing precedes 5- and 3-end processing in human cells unlike in yeast.

molecular biology↗

bioRxiv2021

Inhibition of Mul1-mediated ubiquitination promotes mitochondria-associated translation

G-Protein Pathway Suppressor 2 (GPS2) was recently identified as an endogenous inhibitor of non-proteolytic ubiquitination mediated by the E2 ubiquitin-conjugating enzyme Ubc13. GPS2-mediated restriction of K63 ubiquitination is associated with the regulation of insulin signaling, inflammation and mitochondria-nuclear communication, however a detailed understanding of the targets of GPS2/Ubc13 activity is currently lacking, Here, we have dissected the GPS2-regulated K63 ubiquitome in mouse embryonic fibroblasts and human breast cancer cells, unexpectedly finding an enrichment for proteins involved in RNA binding and translation. Characterization of putative targets, including the RNA-binding protein PABPC1 and translation factor eiF3m, revealed a strategy for regulating the mitochondria-associated translation of selected mRNAs via Mul1-mediated ubiquitination. Our data indicate that removal of GPS2-mediated inhibition, either via genetic deletion or stress-induced nuclear translocation, promotes the ubiquitination of mitochondria-associated translation factors leading to increased expression of an adaptive antioxidant program. In light of GPS2 role in nuclear-mitochondria communication, these findings reveal an exquisite regulatory network for modulating mitochondrial gene expression through spatially coordinated transcription and translation.

cell biology↗

bioRxiv2021

Mechanisms of translation inhibition and suppression of Stress Granule formation by cisplatin

Platinum-based antineoplastic drugs, such as cisplatin, are commonly used to induce tumor cell death. Cisplatin is believed to induce apoptosis as a result of cisplatin-DNA adducts that inhibit DNA and RNA synthesis. Although idea that DNA damage underlines anti-proliferative effects of cisplatin is dominant in cancer research, there is a poor correlation between the degree of the cell sensitivity to cisplatin and the extent of DNA platination. Here, we propose a novel mechanism of cisplatin-mediated cytotoxicity. We show that cisplatin suppresses formation of Stress Granules (SGs), pro-survival RNA granules with multiple roles in cellular metabolism. Mechanistically, cisplatin inhibits cellular translation to promote disassembly of polysomes and aggregation of ribosomal subunits. As SGs are in equilibrium with polysomes, cisplatin-induced shift towards ribosomal aggregation suppresses SG formation and promotes cellular death. Our data also explain nephrotoxic, neurotoxic and ototoxic effects of cisplatin treatment.

cell biology↗

bioRxiv2020

A Novel Stress Response Pathway Regulates Ribosome Biogenesis

Production of ribosomes is an energy-intensive process owing to the intricacy of these massive macromolecular machines. Each human ribosome contains 80 ribosomal proteins and four non-coding RNAs. Accurate assembly requires precise regulation of protein and RNA subunits. In response to stress, the integrated stress response (ISR) rapidly inhibits global translation. How rRNA is coordinately regulated with the rapid inhibition of ribosomal protein synthesis is not known. Here we show that stress specifically inhibits the first step of rRNA processing. Unprocessed rRNA is stored within the nucleolus, and, when stress resolves, it re-enters the ribosome biogenesis pathway. Retention of unprocessed rRNA within the nucleolus aids in the maintenance of this organelle. This response is independent of the ISR or inhibition of cellular translation but represents an independent stress-response pathway that we term Ribosome Biogenesis Stress Response (RiBiSR). Failure to coordinately regulate ribosomal protein translation and rRNA production results in nucleolar fragmentation. Our study unveils a novel stress response pathway that aims at conserving energy, preserving the nucleolus, and prevents further stress by regulation of rRNA processing.

biochemistry↗

bioRxiv2019

Regulation of FXR1 by alternative splicing is required for muscle development and controls liquid-like condensates in muscle cells

Fragile-X mental retardation autosomal homolog-1 (FXR1) is a muscle-enriched RNA-binding protein. FXR1 depletion is perinatally lethal in mice, Xenopus, and zebrafish; however, the mechanisms driving these phenotypes remain unclear. The FXR1 gene undergoes alternative splicing, producing multiple protein isoforms and mis-splicing has been implicated in disease. Furthermore, mutations that cause frameshifts in muscle-specific isoforms result in congenital multi-minicore myopathy. We observed that FXR1 alternative splicing is pronounced in the serine and arginine-rich intrinsically-disordered domain; these domains are known to promote biomolecular condensation. Here, we show that tissue-specific splicing of fxr1 is required for Xenopus development and alters the disordered domain of FXR1. FXR1 isoforms vary in the formation of RNA-dependent biomolecular condensates in cells and in vitro. This work shows that regulation of tissue-specific splicing can influence FXR1 condensates in muscle development and how mis-splicing promotes disease.\n\nHIGHLIGHTSO_LIThe muscle-specific exon 15 impacts FXR1 functions\nC_LIO_LIAlternative splicing of FXR1 is tissue- and developmental stage specific\nC_LIO_LIFXR1 forms RNA-dependent condensates\nC_LIO_LISplicing regulation changes FXR1 condensate properties\nC_LI

cell biology↗

bioRxiv2019

Multiple ribonuclease A family members cleave transfer RNAs in response to stress

During stress, changes in gene expression are critical for cell survival. Stress-induced tRNA cleavage has been implicated in various cellular processes, where tRNA fragments play diverse regulatory roles. Angiogenin (ANG), a member of the RNase A superfamily, induces cleavage of tRNAs resulting in the formation of tRNA-derived stress-induced RNAs (tiRNAs) that contribute to translational reprogramming aiming at cell survival. The role of other stress-induced RNases in tRNA cleavage is poorly understood. Using gene editing and biochemical approaches, we show that other members of the RNase A family are capable of targeting tRNAs in stress-responsive manner. We show that in the absence of ANG, these RNases also promote the production of tiRNAs. Moreover, specific stresses (such as treatment with sodium arsenite) activate cleavage of universal 3-CCA termini of tRNAs in ANG-independent fashion in living cells. We conclude that multiple RNase A family members are capable of targeting tRNAs in a stress-specific manner in vivo.

molecular biology↗