Biology subjects

Sultana, S.

Publications and source records attributed to Sultana, S..

At least 19 recordsLinked to original sources

bioRxiv2026

RAP2.6 negatively regulates Arabidopsis submergence tolerance through GSNOR1-dependent redox and hormonal signaling

Group VII ETHYLENE RESPONSE FACTORs (ERFVIIs) are central regulators of plant responses to oxygen deprivation. However, the contributions of many other APETALA2 (AP2)/ERF transcription factors to hypoxia and flooding responses remain poorly understood. Here, we identify the group X ERF transcription factor RAP2.6 as a negative regulator of submergence tolerance in Arabidopsis thaliana. RAP2.6 expression declined under hypoxia, and plants overexpressing RAP2.6 exhibited reduced survival following dark submergence, whereas the rap2.6-1 loss-of-function mutant showed enhanced tolerance to submergence, hypoxia, and ethanol treatment. Enhanced tolerance of rap2.6-1 was associated with reduced membrane injury, maintenance of photosynthetic pigments and soluble sugars, and extensive metabolic remodeling. RAP2.6 overexpression altered nitric oxide (NO), S-nitrosothiol (SNO), and ethylene accumulation during submergence and was associated with greater oxidative damage and enhanced abscisic acid (ABA)-responsive gene expression. Genetic analyses using S-NITROSOGLUTATHIONE (GSNO) REDUCTASE 1 (GSNOR1) gain- and loss-of-function backgrounds demonstrated that GSNOR1-dependent GSNO homeostasis strongly modified RAP2.6-dependent submergence responses. Increased GSNOR1 activity suppressed the submergence-sensitive phenotype of RAP2.6-overexpressing plants, reduced nitro-oxidative stress, and restored carbohydrate reserves, whereas loss of GSNOR1 activity abolished the enhanced tolerance of rap2.6-1. GSNOR1 also modified RAP2.6-dependent expression of genes associated with oxygen sensing and ABA signaling, while its protective effect was not explained solely by changes in ethylene accumulation. Together, these findings identify RAP2.6 as a regulatory component of the low-oxygen response and reveal a functional interaction between RAP2.6 and GSNOR1-dependent redox signaling that coordinates plant hormonal, metabolic, and oxidative responses during submergence.

plant biology↗

bioRxiv2026

Molecular characterization of required for killing-2: a gene required for spore killing by Neurospora Sk-3.

The Sk-3 selfish genetic element in Neurospora fungi is transmitted to offspring in a biased manner through spore killing. In crosses between an Sk-3 strain and a Spore killing-sensitive (Sk-S) strain, nearly all offspring that fail to inherit Sk-3 are killed. Although a mutation called rfk-2UV, which disrupts spore killing by Sk-3, was isolated in an earlier work, its precise location within the Sk-3 element was not identified. Here, we demonstrate that rfk-2UV is a T>G transversion mutation within a protein coding gene called rfk-2. The rfk-2 gene is located on Chromosome III, and it encodes a transcript that undergoes RNA splicing and at least two RNA editing events. One of these editing events changes a UAG stop codon to a UGG tryptophan codon and allows for production of a 102 amino acid protein. Additionally, while our results demonstrate that rfk-2 is required for spore killing, they also show that it is insufficient for the process. Sk-3 is thus more complex than previously anticipated. Rather than using a single gene to produce its killer, Sk-3 requires multiple genes to kill spores and break the rules of Mendelian Inheritance.

genetics↗

bioRxiv2026

Host-secreted lactate during respiratory viral infection diminishes macrophage antibacterial activity through metabolic reprogramming

In polymicrobial infections, how the host recognizes and responds to pathogens influences which species will persist to cause chronic infections. The human respiratory tract is a common anatomical site for viral-bacterial co-infections, where primary viral infections predispose to secondary bacterial infections, leading to increased morbidity and mortality. Additionally, co-infections are disproportionately prevalent in people with chronic lung diseases, such as chronic obstructive pulmonary disease and cystic fibrosis. We previously reported that primary viral infections and antiviral interferon (IFN) signaling stimulate Pseudomonas aeruginosa (PA) biofilm formation on airway epithelial cells (AECs). IFN signaling induces aerobic glycolysis in AECs and generates lactate as a cellular byproduct. Given that innate immune systems play an integral role in co-infection dynamics, we investigated the role of host-secreted metabolites (i.e. lactate) on innate immune cell activity during respiratory co-infections. We found that exposure to the apical secretions from IFN{beta}-treated AECs significantly compromised macrophage antibacterial activity, with the soluble metabolite lactate playing an important role. Macrophages used monocarboxylate transporters and G-protein receptors to transport and/or sense lactate, respectively, and this exposure to lactate diminished their bacterial-killing activity in a time-exposure dependent manner. Lactate exposure particularly reprogrammed macrophage cellular metabolism towards an anti-inflammatory state by increasing oxidative phosphorylation and fatty acid oxidation. Collectively, these findings provide insight into metabolites as complex regulators of trans-kingdom interactions and epithelial-macrophage crosstalk during respiratory co-infections.

immunology↗

bioRxiv2026

Characterization of Chromium-Resistant and Reducing Bacteria from Poultry Litter Ecosystems

Compact poultry raising has turned poultry litter into an environmental problem, as it may all be packed with heavy metals and drug-resistant germs. Of all the metals, chromium contamination not only disturbs the general environment but is also a source of concern for public health. Poultry litters were taken from 14 farms in different places, and the bacteria characters from different places were tested for their capacity to tolerate Cr(VI). A total of 31 bacterial isolates were initially screened, and three of them (AH-2, AZ-1, and AMF-3) appeared to be very resistant to chromium. The isolates were able to survive at the highest concentration, 800 mg/L of the Cr(VI); however, AH-2 was the most resistant one (MIC: 900 mg/L; MBC: 1000 mg/L). Chromium reduction tests showed that AMF-3 at high concentration showed the maximum chromium reduction, while AH-2 achieved higher chromium reduction at medium concentration. Phenotypic and biochemical analysis showed that the isolates were Staphylococcus spp., which was confirmed by 16S rRNA gene sequencing as S. cohnii, S. saprophyticus, and S. gallinarum. Moreover, chromium was detected at higher levels in poultry litter compared to the feed, with the highest accumulation in AZ farm litter (4464.0 g/kg). The highlighting feature of our article is the presence of chromium-tolerant and reducing bacteria in poultry environments. Besides that, the level of chromium in poultry litter is really high, and it points to the need for better waste management.

microbiology↗

bioRxiv2026

FTO-Dependent m6A RNA Dysregulation Underlies Memory Deficits Induced by Early-Life Stress

Cognitive functions in adults are mainly attributed to experience-dependent plasticity. Nonetheless, the developmental encoding of memory deficits is still inadequately addressed. Here, we demonstrate that early-life stress (ELS) reprograms the hippocampal epitranscriptome by enhancing N6-methyladenosine (m6A) deposits during early development leading to memory deficit in adulthood. We observed a shift toward hypermethylation of transcripts including coding and non-coding RNAs (lncRNAs) following maternal separation. We also observed that these transcripts encoding proteins necessary for translational regulation, ribosome biogenesis and mitochondrial function. This epitranscriptomic change is driven by ELS-induced downregulation of the m6A demethylase FTO (Fat mass and obesity-associated protein). We observe that the overexpression of FTO in young adult mice selectively rescues memory deficits without ameliorating elevated anxiety. Further, the knockdown of FTO in primary hippocampal neuron, mimicking ELS - induced reduction of its expression, leads to reduced translation as detected by puromycin labelling. Taken together, our study demonstrated previously uncharacterized mechanism of ELS-induced epitranscriptomic change linked with memory deficit via the regulation of protein synthesis.

neuroscience↗

bioRxiv2026

A newly identified detoxification system protects uropathogenic Escherichia coli from reactive chlorine species

Neutrophils eliminate invading pathogens through the production of reactive oxygen and chlorine species (ROS/RCS), with hypochlorous acid (HOCl) representing the most abundant and bactericidal oxidant produced in this process. Compared to bacterial defenses against ROS, which are well studied, little is known about how pathogens respond to and counter RCS, including HOCl. Here, we identify and mechanistically characterize RcrB, a protein of the uncharacterized DUF417 protein family, for which no role in oxidative stress defense has been described yet. We report a previously unrecognized role as an RCS detoxification system that confers high-level resistance to uropathogenic Escherichia coli (UPEC). We show that RcrB is an inner membrane protein and strongly induced during RCS exposure and phagocytosis. Loss of RcrB results in profound HOCl hypersensitivity, accompanied by elevated macromolecular damage and severe metabolic perturbations, establishing RcrB as a central determinant of UPECs RCS stress resistance. Heterologous expression of RcrB in HOCl-sensitive intestinal E. coli strains is sufficient to restore resistance but requires functional glutathione biosynthesis. Quantitative HOCl trapping assays demonstrate that RcrB expression protects the bacterial population by significantly reducing extracellular HOCl, indicating active chemical quenching rather than passive membrane protection. Structure-function analysis of RcrB confirms this conclusion and demonstrate that conserved, redox-active amino acids facing the periplasm are essential for its detoxification activity. In summary, our study reveals a hitherto unknown bacterial strategy for mitigating RCS and reveal a distinct mechanism by which UPEC may survive the mammalian host defense. Significance StatementDuring infection, human immune cells such as neutrophils kill bacteria by releasing powerful oxidants, including hypochlorous acid (HOCl), the active ingredient of household bleach. How pathogenic bacteria survive this chemical attack is still poorly understood. This study identifies a membrane protein in uropathogenic Escherichia coli as a key defense factor that neutralizes HOCl before it can damage the cell. RcrB acts at the bacterial cell envelope, where it detoxifies HOCl in a glutathione-dependent manner to maintain a balanced redox homeostasis and cellular integrity, thereby even protect neighboring bacteria. These findings reveal a previously unrecognized frontline defense strategy that helps pathogens survive immune attack and may represent a new target for antimicrobial therapies.

microbiology↗

bioRxiv2026

MDA5 multimerization on LINE RNA drives pathogenic extracellular immune complexes in autoimmunity

Autoantibodies are hallmarks of many autoimmune diseases, but their potential pathogenic roles, particularly for those targeting intracellular proteins, remain unclear. Anti-MDA5-positive dermatomyositis (anti-MDA5 DM) is characterized by autoantibodies against the intracellular protein MDA51,2, a conserved innate immune receptor that recognizes viral dsRNA by forming filaments3. Here, using four patient-derived monoclonal autoantibodies (mAbs), we reconstitute and define the molecular architecture, biogenesis, and immunological activity of pathogenic MDA5 immune complexes. Our cryo-EM analysis revealed that these mAbs bind dsRNA-scaffolded MDA5 filaments in at least two distinct binding modes, each exhibiting striking epitope convergence using germline-encoded residues. Extracellular immune complexes formed between mAbs and filamentous, but not monomeric, MDA5 potently activate multiple innate immune pathways, with the magnitude of activation determined by antibody binding mode and immune complex stoichiometry. Antibody bivalency further crosslinks MDA5 filaments into higher-order aggregates with heightened immunostimulatory activity, demonstrating an active role of autoantibodies in shaping immune complex architecture. Analysis of patient plasma reveals elevated levels of extracellular MDA5 filaments and identifies LINE retroelement-derived dsRNA as a structural scaffold. Notably, MDA5 immune complexes induce endogenous LINE dsRNA expression, likely promoting additional MDA5 filament formation and extracellular release through inflammatory cell death. These data thus support a self-amplifying inflammatory cycle as a pathogenic mechanism for anti-MDA5 DM. Collectively, our study defines a broadly applicable architectural principle, in which higher-order organization and binding modes of autoantibodies--beyond antibody affinity or nucleic acid presence alone--govern innate immune activation.

biochemistry↗

bioRxiv2025

The anti-retroviral therapy emtricitabine affects skeletal muscle DNA methylation and transcriptome patterns in a male HIV mouse model

BackgroundAlthough antiretroviral therapies (ART) have substantially reduced HIV-associated mortality, the increased lifespan achieved by widespread ART deployment has revealed that HIV infection is linked to an unexplained earlier onset and increased incidence of aging-associated conditions like sarcopenia. Complex syndromes, like sarcopenia, often arise from a combination of genetic and environmental factors, so in this study, we investigated effects of short-term treatment with emtricitabine (2,3-dideoxy-5-fluoro-3-thiacytidine; FTC), an FDA approved ART, on skeletal muscle DNA methylation patterns and transcriptome-wide responses in a male murine model of HIV phenotypic biology (Tg26 mice). MethodsWe treated 6 month old male Tg26 (+/-) mice or wildtype (WT) littermates on a C57BL/6 genetic background with FTC in the drinking water for one month; control groups received drinking water vehicle alone (VEH). Muscle function and body composition were measured longitudinally. Skeletal muscle methylation patterns, transcriptional changes, and histological features were quantified at sacrifice. ResultsAlthough neither gross structural nor functional muscle deficits were observed in this short-term study with ART usage, relative decreases in muscle endurance measured by hang time over the study were 2-fold more severe in the Tg26 as compared to WT mice (p=0.0453), and markers of myogenic cell maturation (Myf5, Myf6) were disrupted in the Tg26 HIV model as compared to WT littermates in a manner exacerbated by FTC treatment. Fat mass, measured by DXA, also tended (p=0.085) to be uniquely increased by FTC treatment in the Tg26 mice over the study. Differential methylation patterns and pathway enrichment data suggested that the presence of an HIV phenotype and exposure to an ART regimen altered the methylation status in skeletal muscle genes such as Camk2B, Pcolce2 and Lima1 in a manner consistent with promoting eventual functional impairment in muscle. Additionally, RNAseq revealed differential gene expression profiles and key regulatory pathways including cellular differentiation, regulation of lipid metabolism, and neuroactive ligand-receptor interactions. Lipodystrophy-related genes including LEP, ADIPOQ and PPAR involved in fat distribution and metabolism along with skeletal genes related to regulation of muscle strength were affected by the presence of an HIV phenotype and ART treatment. ConclusionsThe current study provides insights into mechanisms by which a clinically relevant ART may influence DNA methylation and transcriptome changes in skeletal muscle in the context of HIV biology. The differentially regulated pathways suggest novel targets for understanding, and eventually abrogating, the harmful effects of long-term ART use in PLWH on skeletal muscle mass and function.

cell biology↗

bioRxiv2025

Local translation of circular RNAs is required for synaptic activity and memory

Circular RNAs (circRNAs) are enriched in synapses and implicated in cognitive processes, and recent studies have shown that circRNAs can encode micropeptides, which suggests that there may be novel synaptic proteoforms in the brain that await discovery. Here we report widespread learning-induced local circRNA translation in the prefrontal cortex of male C57BL/6 mice. More than 1500 synapse-enriched circRNAs contain active IRES elements, with 842 interacting with the ribosome and 241 exhibiting direct evidence of activity-induced translation. We discovered a synapse-enriched micropeptide (P1) that is derived from a single exon circRNA, the mRNA host of which encodes an enzyme associated with protein repair. Although P1 is only a third of the size of the full-length protein, it is locally expressed, enzymatically active, and interacts with plasticity-related proteins, including CaMKII. In addition to direct effects on synaptic activity, targeted P1 knockdown impairs whereas its overexpression enhances fear extinction memory. These findings shed new light on the dark proteome in the brain and reveal local circRNA translation as a novel mechanism of plasticity and memory.

neuroscience↗

bioRxiv2025

Environmental and Maternal Imprints on Infant Gut Metabolic Programming

Early life is a critical period for immune and metabolic programming, but developmental patterns remain underexplored in populations from low- and middle-income countries. Here, we profiled the microbiome and metabolome of 55 Bangladeshi mother-infant dyads over the first six months of life. Importantly, we observed an increase in microbially-derived bile amidates and N-acyl lipids with age in conjunction with reads matching the bile salt hydrolase/transferase (bsh) gene. While microbial source tracking confirmed maternal fecal seeding, a substantial environmental contribution was also highlighted. Differences in infant fecal metabolic profiles were associated with delivery mode, maternal milk composition, household assets, and household-level water treatment. C-section delivery and untreated drinking water were linked to transient metabolic differences, including increases in bile amidates, N-acyl lipids, and other host-microbe co-metabolic products, including acylcarnitines. Multi-omics analysis revealed specific microbial-metabolite relationships, highlighting how early environmental and maternal living circumstances shape metabolic gut programming through the microbiome.

microbiology↗

bioRxiv2025

Protein Barcoding and Next-Generation Protein Sequencing for Multiplexed Protein Selection, Analysis, and Tracking

Protein barcoding has emerged as a powerful tool for the multiplexed identification and characterization of proteins, providing a mechanism for precise tracking of protein affinity, location, and expression. In this study, we describe the development of a protein barcoding workflow for use with single-molecule Next-Generation Protein Sequencing (NGPS) on the benchtop Platinum(R) and Platinum(R) Pro instruments. We present data on the validation of eight peptide barcodes, each designed to minimize detection bias and maximize sensitivity across various experimental conditions. We have also optimized the design of expression constructs to decrease both the hands-on time and input requirements of the workflow. In this workflow, affinity-tagged proteins are expressed with unique peptide barcodes. Following experimental selection or treatments, the proteins are purified, and the peptide barcodes are cleaved and sequenced on the Platinum instrument. We demonstrate that we can detect barcodes at 400 fmol of sample input concentration within the eight-plex mixture, and at 50 fmol of sample input for individual barcodes. We also show the capacity of this barcoding approach to achieve a ten-fold dynamic range, underscoring its sensitivity in recovering variants with low abundance. Through the combination of protein barcoding and NGPS, we lay the groundwork for future studies aimed at characterizing protein interactions and improving targeted drug delivery strategies.

biochemistry↗

bioRxiv2024

MATRIN3 deficiency triggers autoinflammation via cGAS-STING activation

Interferon-stimulated genes (ISGs) comprise a program of immune effectors important for host immune defense. When uncontrolled, ISGs play a central role in interferonopathies and other inflammatory diseases. The mechanisms responsible for turning on ISGs are not completely known. By investigating MATRIN3 (MATR3), a nuclear RNA-binding protein mutated in familial ALS, we found that perturbing MATR3 results in elevated expression of ISGs. Using an integrative approach, we elucidate a pathway that leads to activation of cGAS-STING. This outlines a plausible mechanism for pathogenesis in a subset of ALS, and suggests new diagnostic and therapeutic approaches for this fatal disease. One-Sentence SummaryMis-splicing of Tudor Domain Containing 3 (TDRD3) in the absence of MATR3 unleashes R-loops and interferon-stimulated genes.

molecular biology↗

bioRxiv2024

Identification of Thioredoxin1 interacting proteins in neuronal cytoskeletal organization during autophagy

Thioredoxin1 (Trx1) is a major cytoplasmic thiol oxidoreductase protein involved in redox signaling. This function is rendered by a rapid electron transfer reaction during which Trx1 reduces its substrate and itself becomes oxidized. In this reaction, Trx1 forms a transient disulfide bond with the substrate which is unstable and therefore identification of Trx1 substrates is technically challenging. This process maintains the cellular proteins in a balanced redox state and ensures cellular homeostasis. Trx1 levels are reduced in some neurodegenerative diseases; therefore, understanding the interactions between Trx1 and its substrates in neurons could have significant therapeutic implications. We utilized a transgenic mouse model expressing a Flag-tagged mutant form of Trx1 that can form stable disulfide bonds with its substrates allowing identification of the Trx1 interacting proteins. The involvement of Trx1 has been suggested in autophagy, we aimed to investigate Trx1 substrate after pharmacologic induction of autophagy in primary hippocampal neurons. Treatment of primary neurons by rapamycin, a standard autophagy inducer, caused significant reduction of neurite outgrowth and alterations in the cytoskeleton. Through immunoprecipitation and mass spectrometry, we have identified 77 Trx1 interacting proteins which were associated with a wide range of cellular functions including a major impact on cytoskeletal organization. The results were confirmed in Trx1 knocked-down cells and in nucleofected primary neurons. Our study suggests a novel role for Trx1 in regulation of neuronal cytoskeleton organization, marking the first investigation of Trx1-interacting proteins in primary neurons and confirming the multifaceted role of Trx1 in physiological and pathological states.

biochemistry↗

bioRxiv2024

Increased capacity to maintain glucose homeostasis in a transgenic mouse expressing human but not mouse growth hormone with developing high fat diet-related insulin resistance, steatosis and adipose dysfunction

ObjectiveDifferences in primate and non-primate growth hormone (GH) genes can affect their regulation and function. This includes the ability of human (h) but not mouse (m) GH to bind the prolactin (PRL) receptor (PRLR) as well as the GH receptor (GHR). Potential differential effects were assessed in male hGH- or mGH-expressing mice and fed high fat diet (HFD) versus regular chow diet (RCD). Pancreas and epididymal white adipose tissue (eWAT) gene expression and/or related function were targeted as the pancreas responds to both PRLR and GHR signaling and catabolic effects like lipolytic activity are more directly attributable to GH and GHR signaling. DesignA transgenic CD-1 mouse expressing hGH but not mGH under hypothalamic control was generated to compare with wild type CD-1 mice and size and bone density determined. Glucose clearance, islet area, insulin and insulin-like growth factor (IGF) -2 gene expression were assessed as well as serum glucose and insulin levels in mice fed a HFD versus RCD for 8 and 24 weeks. Adiposity, liver and serum triglycerides as well as eWAT cell area, cytokine (leptin and adiponectin) and senescence-related marker (p21CIP1 and p16INK4a) RNA levels were also assessed. ResultsMale hGH-expressing transgenic CD-1[{Delta}mGH.hGH] mice have significantly lower liver IGF-1 RNA levels and are smaller based on length and weight than wild type CD-1[mGH] mice. They also have [~]1.5-fold higher total body fat and serum triglyceride levels. However, CD-1[{Delta}mGH.hGH] and CD-1[mGH] mice grow at the same rate with similar cortical and trabecular bone densities. Unlike CD-1[mGH] mice, there was no significant delay in glucose clearance in CD-1[{Delta}mGH.hGH] mice after 8 weeks on a HFD versus RCD; while basal (RCD) serum insulin levels were similar, fasting glucose levels were lower and pancreas IGF-2 RNA levels were increased in CD-1[{Delta}mGH.hGH] mice. However, both CD-1[{Delta}mGH.hGH] and CD-1[mGH] showed evidence of increased insulin resistance after 24 weeks on HFD, including delayed glucose clearance in spite of increased pancreatic islet area and insulin production as well as signs of liver steatosis and increased hepatic triglyceride levels. These increases correlated with elevated PRLR but not GHR RNA levels. Assessment of eWAT revealed >2-fold larger adipocytes in CD-1[{Delta}mGH.hGH] compared to CD-1 [mGH] mice fed RCD at both 12 and 28 weeks. This was associated with an [~]2.6-fold increase in leptin RNA levels at 12 weeks and [~]58% lower adiponectin RNA levels at 28 weeks. A >2-fold increase in p21CIP1 transcript levels was also detected in eWAT from both CD-1[{Delta}mGH.hGH] and CD-1 [mGH] mice fed RCD with age (28 versus 12 weeks) but were unaffected by diet. However, a >2-fold increase in p16INK4a RNA levels was observed after 24 weeks on HFD. ConclusionsWhile limited to observations in the male, transgenic CD-1[{Delta}mGH.hGH] mice exhibit signs of GH insufficiency and eWAT adipocyte dysfunction. These mice also show an initial resistance to the negative effects of HFD on glucose clearance when compared to CD-1[mGH] mice, which is potentially related to a differential effect of hGH versus mGH on pancreas development and/or function.

physiology↗

bioRxiv2023

Gas5 regulates early life stress-induced anxiety and spatial memory

Early life stress (ES) induced by maternal separation (MS) remains a proven causality of anxiety and memory deficits at later stages of life. Emerging studies have shown that MS-induced gene expression in the hippocampus is operated at the level of transcription. However, the extent of involvement of non-coding RNAs in MS-induced behavioural deficits remains unexplored. Here, we have investigated the role of synapse-enriched long non-coding RNAs (lncRNAs) in anxiety and memory upon MS. We observed that MS led to an enhancement of expression of the lncRNA Gas5 (Growth Arrest Specific-5) in the hippocampus; accompanied by increased levels of anxiety and deficits in spatial memory. Gas5 knockdown in early life was able to reduce anxiety and partially rescue the spatial memory deficits of maternally separated adult mice. However, the reversal of MS-induced anxiety and memory deficits is not attributed to Gas5 activity during neuronal development as Gas5 RNAi did not influence spine development. Gene Ontology analysis revealed that Gas5 exerts its function by regulating RNA metabolism and translation. Our study highlights the importance of MS-regulated lncRNA in anxiety and spatial memory.

neuroscience↗

bioRxiv2023

Transcriptomic analysis identifies synapse-enriched lncRNAs required for glutamatergic synapse development and fear memory consolidation.

Regulatory functions of lncRNAs in neurons have been majorly limited to the nucleus. The identity of synaptic lncRNAs and their functional roles associated with synapse development and plasticity are poorly understood. Transcriptomic analysis from synaptoneurosomes identified 94 synapse-enriched lncRNAs from the mouse hippocampus. We find Pvt1 to be a specific regulator of excitatory, not inhibitory, synapse development. Synapse-specific loss of Pvt1 regulates synaptic activity and the downregulation of mRNAs pertinent to synapse development. We also report a synapse-centric role for an uncharacterized lncRNA; 2410006H16Rik (SynLAMP); in translation and memory formation. SynLAMP demonstrates enhanced localization to the synapse following fear conditioning and regulates dendritic translation by sequestering the translation repressor FUS; acting as a molecular decoy. Synapse-specific knockdown of SynLAMP inhibits the localised, activity-dependent translation of CamK2a, a FUS target. SynLAMP RNAi occludes fear-memory formation. Comprehensively, our study highlights that de novo activity of lncRNAs are involved in diverse synaptic functions.

neuroscience↗

bioRxiv2023

Expression of RcrB confers resistance to hypochlorous acid in uropathogenic Escherichia coli

To eradicate bacterial pathogens, neutrophils are recruited to the sites of infection, where they engulf and kill microbes through the production of reactive oxygen and chlorine species (ROS/RCS). The most prominent RCS is antimicrobial oxidant hypochlorous acid (HOCl), which rapidly reacts with various amino acids side chains, including those containing sulfur and primary/tertiary amines, causing significant macromolecular damage. Pathogens like uropathogenic Escherichia coli (UPEC), the primary causative agent of urinary tract infections (UTIs), have developed sophisticated defense systems to protect themselves from HOCl. We recently identified the RcrR regulon as a novel HOCl defense strategy in UPEC. The regulon is controlled by the HOCl-sensing transcriptional repressor RcrR, which is oxidatively inactivated by HOCl resulting in the expression of its target genes, including rcrB. rcrB encodes the putative membrane protein RcrB, deletion of which substantially increases UPECs susceptibility to HOCl. However, many questions regarding RcrBs role remain open including whether (i) the proteins mode of action requires additional help, (ii) rcrARB expression is induced by physiologically relevant oxidants other than HOCl, and (iii) expression of this defense system is limited to specific media and/or cultivation conditions. Here, we provide evidence that RcrB expression is sufficient to E. colis protection from HOCl and induced by and protects from several RCS but not from ROS. RcrB plays a protective role for RCS-stressed planktonic cells under various growth and cultivation conditions but appears to be irrelevant for UPECs biofilm formation. IMPORTANCEBacterial infections pose an increasing threat to human health exacerbating the demand for alternative treatment options. UPEC, the most common etiological agent of urinary tract infections (UTIs), are confronted by neutrophilic attacks in the bladder, and must therefore be well equipped with powerful defense systems to fend off the toxic effects of RCS. How UPEC deal with the negative consequences of the oxidative burst in the neutrophil phagosome remains unclear. Our study sheds light on the requirements for the expression and protective effects of RcrB, which we recently identified as UPECs most potent defense system towards HOCl-stress and phagocytosis. Thus, this novel HOCl-stress defense system could potentially serve as an attractive drug target to increase the bodys own capacity to fight UTIs.

microbiology↗

bioRxiv2022

Species-specific protein-protein interactions govern the humanization of the 20S proteasome in yeast

Yeast and humans share thousands of genes despite a billion years of evolutionary divergence. While many human genes can functionally replace their yeast counterparts, nearly half of the tested shared genes cannot. For example, most yeast proteasome subunits are humanizable, except subunits comprising the {beta}-ring core, including {beta}2 (HsPSMB7). We developed a high-throughput pipeline to humanize yeast proteasomes by generating a large library of Hs{beta}2 mutants and screening them for complementation of yeast {beta}2 (ScPup1). Variants capable of replacing ScPup1 included (1) those impacting local protein-protein interactions (PPIs), with most affecting interactions between the {beta}2 C-terminal tail and the adjacent {beta}3 subunit, and (2) those affecting {beta}2 proteolytic activity. Exchanging the full-length tail of human {beta}2 with that of ScPup1 enabled complementation. Moreover, wild-type human {beta}2 replaced yeast {beta}2 if the adjacent human {beta}3 subunit was also provided. Unexpectedly, yeast proteasomes bearing a catalytically inactive HsPSMB7-T44A variant blocking precursor autoprocessing were viable, suggesting an intact propeptide stabilizes late assembly intermediates. Our data reveal roles for specific PPIs governing functional replaceability across vast evolutionary distances.

genetics↗