Biology subjects

Huynh, T. N.

Publications and source records attributed to Huynh, T. N..

16 recordsLinked to original sources

bioRxiv2026

Mutations in MreB suppress β-lactam sensitivity upon c-di-AMP accumulation in Listeria monocytogenes

Cyclic di-AMP (c-di-AMP) is an essential second messenger in Listeria monocytogenes, but its accumulation is detrimental as it disrupts cell wall homeostasis and attenuates virulence. The mechanisms underlying this toxicity remain poorly understood. To understand the molecular basis of this toxicity, we performed a forward genetic screen to identify suppressor mutations that restore {beta}-lactam resistance in a {Delta}pdeA {Delta}pgpH ({Delta}PDE) mutant, which accumulates high c-di-AMP and is susceptible to cell wall-targeting {beta}-lactam antibiotics. We found that the majority of suppressor mutants carried mutations in the mreB gene, which encodes the bacterial actin-like cytoskeletal protein, MreB, that directs lateral peptidoglycan synthesis during cell elongation. These mutations restored {beta}-lactam resistance and ex vivo virulence while still retaining high intracellular c-di-AMP levels. Microscopy analyses indicate that these suppressor mutations reduce MreB activity, as evidenced by cell widening, and that they phenocopy sublethal treatment with the MreB inhibitor A22. Consistently, A22 treatment also rescued {beta}-lactam sensitivity in the {Delta}PDE mutant, supporting a functional link between MreB activity and c-di-AMP toxicity. Mechanistically, c-di-AMP accumulation impaired cell division/septation and reduced peptidoglycan synthesis under cell wall stress, whereas MreB mutations restored both transglycosylation and transpeptidation activities and promoted cell division. These effects were independent of potassium homeostasis, suggesting a distinct pathway linking c-di-AMP to cell wall regulation in L. monocytogenes. Together, our findings demonstrate that dysregulated MreB activity contributes to cell wall defects at elevated c-di-AMP levels and highlight the importance of coordinating cytoskeletal dynamics with cell division to maintain cell envelope integrity.

microbiology↗

bioRxiv2026

Listeria monocytogenes prophage induction is activated by ppGpp and inhibited by c-di-AMP

Bacteriophages, particularly temperate prophages that integrate directly into the host genome, are crucial drivers of bacterial evolution and act as fundamental architects of microbial communities. Listeria monocytogenes 10403S has two phage elements - prophage {Phi}10403S and monocin element. In this study, we found that c-di-AMP, a crucial second messenger in L. monocytogenes, regulates phage production. C-di-AMP accumulation down-regulates the gene expression of prophage and monocin gene loci and inhibits phage production, both spontaneous phage production as well as under phage induction through mitomycin-C treatment. We found that in genetically heterogenous cultures, super-infection of non-lysogenic strains with phage-containing strains can significantly amplify spontaneous prophage production. Using these cultures as an induction system, we found other inducers of spontaneous phage production. We found that ppGpp accumulation and nutrient starvation acts as an inducer of the spontaneous prophage production in L. monocytogenes. H2O2 can also play a role in inducing spontaneous phage production. Moreover, {Phi}10403S prophage production is suppressed in co-cultures of L. monocytogenes 10403S with L. monocytogenes F2365 and L. innocua CLIP11262. ImportanceMost Listeria and L. monocytogenes strains are lysogens, although the impact of phage genes on bacterial host metabolism or host fitness during bacterial competition is still unexplored. Bacteriophages have been shown to influence the evolution of their host and, in several cases, have a major effect on environmental fitness, pathogenicity and/or virulence of bacterial pathogens, either by regulating expression of critical genes or encoding beneficial genes. Prophages provide their hosts with a competitive edge through lysogenic conversion-- introducing novel toxins and defense systems--while simultaneously maintaining a molecular trigger, in the form of lysogenic-to-lytic switch, capable of initiating population-wide lysis in response to environmental stress. In the human pathogen Listeria monocytogenes, these prophages are near-ubiquitous and studies by other groups have described them as critical regulators of the bacteriums SOS pathways and its pathogenic lifestyle. This study identifies important novel regulators of phage induction in Listeria monocytogenes - c-di-AMP, ppGpp and H2O2, and how phage induction and production can shape the dynamics of bacterial competition of its host.

microbiology↗

bioRxiv2025

NOD2 modulates MDA5 signaling to promote coxsackievirus B3 replication

Coxsackievirus is an enteric virus that encounters intestinal epithelial cells (IECs) after ingestion and can cause a range of illnesses from mild to severe, including gastroenteritis, pancreatitis, central nervous system diseases and myocarditis. Sensing of CVB3 RNA by melanoma differentiation-associated gene (MDA5) induces a Type 1 Interferon (T1IFN) response that is critical for reducing viral replication and dissemination within cells and the host. The cytosolic nucleotide oligomerization domain-containing protein 2 (NOD2), however, has been implicated in a proviral role in CVB3-induced myocarditis, but the underlying mechanism is not well understood. Because NOD2 is especially important in maintaining intestinal immune homeostasis and CVB3 is an enteric virus that initially infects the intestinal tract leading to virus dissemination to other tissues, we sought to determine whether NOD2 expressed in IECs would impact CVB3 infection. Here, we demonstrate that IEC NOD2 promotes CVB3 replication. Replication of a related Enterovirus, poliovirus, was also enhanced by NOD2. We discovered that NOD2-/- IECs have increased T1IFNs and interferon stimulated gene (ISG) expression, including IFIH1, the gene encoding for MDA5. Replication of CVB3 was rescued when MDA5 expression was reduced in NOD2-/- IECs. CVB3 replication was further increased, and the T1IFN response reduced, in NOD2+/+IECs treated with the mitophagy inducer carbonyl cyanide m-chlorphenyl hydrazone (CCCP). Mitophagy induction in NOD2-/- IECs, however, had no effect on CVB3 replication, or the T1IFN response, suggesting a role for NOD2 in mitophagy. Overall, our data demonstrate that NOD2 promotes CVB3 replication in IECs by suppressing T1IFN expression and MDA5 activation via NOD2-mediated mitophagy. Since T1IFN restricts enteroviruses in vivo, CVB3 and other enteroviruses might exploit NOD2 activation in the intestinal tract to evade antiviral T1IFN responses. This evasion could enhance their replication in the intestine and promote their spread to other organs, potentially leading to diseases in the pancreas, heart, and central nervous system. ImportanceCoxsackievirus B3 (CVB3) is a significant human intestinal virus capable of spreading to other organs. It is closely linked to the development of type I diabetes and can cause severe heart infections, particularly in children. Our research demonstrates that CVB3 exploits the immunity protein NOD2, which usually protects against infections, to infect and replicate in intestinal cells. NOD2 also enhances the replication of poliovirus, another related human enteric virus. When expressed in the intestinal epithelial cells, NOD2 reduces the immune response to certain viral infections by inhibiting expression of the viral sensor MDA5. Overall, CVB3 benefits from NOD2-mediated dampening of antiviral immunity to promote its replication in intestinal cells during fecal-oral transmission.

immunology↗

bioRxiv2024

The microbiota of wooden cheese ripening boards is a rich source of antimicrobial-producing bacteria against Listeria monocytogenes

Wooden boards are essential tools in cheese ripening and there are accumulating observations suggesting their antimicrobial effect against foodborne bacterial pathogens, such as Listeria monocytogenes. However, poor bacterial recovery of bacteria from wood can confound quantification of pathogen burdens. To assess L. monocytogenes survival on wooden cheese boards, we applied a disruptive grinding method and tracked native board-associated bacterial counts as controls. Our data revealed that L. monocytogenes declines on clean zones of wooden boards, but can replicate on areas where there is suitable cheese. Our microbiota analysis revealed diverse bacterial communities on wooden board surfaces, with a prominent presence of Brevibacterium, Brachybacterium, and Staphylococcus genera. We further identified seven bacterial species that inhibit L. monocytogenes, belonging to Bacillus, Staphylococcus, and Serratia phyla, as well as Lactococcus lactis. We focused on a Bacillus safensis isolate as a novel biocontrol agent candidate, and found it to potently inhibit L. monocytogenes via secreted antimicrobial factors. Our genomic, bioinformatic, and biochemical analyses indicate that those factors are likely antimicrobial peptides encoded by multiple biosynthetic gene clusters, several of which are unique to B. safensis and have not been characterized. A sub-inhibitory concentration of B. safensis supernatant induces a significant down-regulation of prophage elements and up-regulation antimicrobial stress response in L. monocytogenes. Taken together, our findings indicate that the wooden board microbiota is a rich source of antimicrobial-producing bacteria with potential applications in foodborne pathogen control strategies. IMPORTANCEDespite stringent food safety measures, L. monocytogenes foodborne outbreaks remain frequent with high hospitalization and mortality rates. Removal of L. monocytogenes from food processing environments is extremely challenging, because this pathogen is ubiquitous and encodes a wide array of stress response mechanisms that enable it to thrive under harsh conditions. Our study found that clean wooden boards used in cheese ripening inhibit L. monocytogenes, causing a noticeable decline in pathogen population following surface inoculation. Bacterial communities on wooden cheese boards are rich and diverse, and harbor many species that produce antimicrobial compounds against L. monocytogenes, with the example of a new B. safensis isolate. Therefore, wooden board microbiota is a promising source for future antimicrobial discovery efforts.

microbiology↗

bioRxiv2024

Inhibiting the cholesterol storage enzyme ACAT1/SOAT1 in aging Apolipoprotein E4 mice alter their brains inflammatory profiles

Aging and Apolipoprotein E4 (APOE4) are the two most significant risk factors for late-onset Alzheimers disease (LOAD). Compared to APOE3, APOE4 disrupts cholesterol homeostasis, increases cholesteryl esters (CEs), and exacerbates neuroinflammation in brain cells including microglia. Targeting CEs and neuroinflammation could be a novel strategy to ameliorate APOE4 dependent phenotypes. Toll-like receptor 4 (TLR4) is a key player in inflammation, its regulation is associated with cholesterol content of lipid rafts in cell membranes. We previously demonstrated that in normal microglia expressing APOE3, inhibiting the cholesterol storage enzyme acylCoA:cholesterol acyltransferase 1 (ACAT1/SOAT1) reduces CEs, dampened neuroinflammation via modulating the fate of TLR4. We also showed that treating myelin debris-loaded normal microglia with ACAT inhibitor F12511 reduced cellular CEs and activated ABC transporter 1 (ABCA1) for cholesterol efflux. In this study, we found that treating primary microglia expressing APOE4 with F12511 also reduces CEs, activated ABCA1, and dampened LPS dependent NFkB activation. In vivo, a two-week injections of nanoparticle F12511, which consists of DSPE-PEG2000, phosphatidylcholine, and F12511, to aged female APOE4 mice reduced TLR4 protein content and decreased proinflammatory cytokines including IL-1{beta} in APOE4 mice brains. Overall, our work suggests nanoparticle F12511 is a novel agent to ameliorate LOAD.

biochemistry↗

bioRxiv2024

Vimentin regulates mitochondrial ROS production and inflammatory responses of neutrophils

The intermediate filament vimentin is present in immune cells and is implicated in proinflammatory immune responses. Whether and how it supports antimicrobial activities of neutrophils is not well established. Here, we developed an immortalized neutrophil model to examine the requirement of vimentin. We demonstrate that vimentin restricts the production of proinflammatory cytokines and reactive oxygen species (ROS), but enhances phagocytosis and swarming. We observe that vimentin is dispensable for neutrophil extracellular trap (NET) formation, degranulation, and inflammasome activation. Moreover, gene expression analysis demonstrated that the presence of vimentin was associated with changes in expression of multiple genes required for mitochondrial function and ROS overproduction. Treatment of wild-type cells with rotenone, an inhibitor for complex I of the electron transport chain, increases the ROS levels. Likewise, treatment with mitoTEMPO, a SOD mimetic, rescues the ROS production in cells lacking vimentin. Together, these data show vimentin regulates neutrophil antimicrobial functions and alters ROS levels through regulation of mitochondrial activity.

immunology↗

bioRxiv2024

Optimized CART Cell Therapy for Metastatic Aggressive Thyroid Cancer

Most thyroid cancer deaths are attributed to a subset of poorly differentiated, metastatic tumors. To improve treatment options for aggressive thyroid cancers, we developed a novel thyroid-stimulating hormone receptor (TSHR)-targeted chimeric antigen receptor T (CART) cell therapy, which demonstrated antigen-specific activation and antitumor efficacy against TSHR+ cell lines in vitro and in vivo. However, de-differentiated thyroid cancers downregulate TSHR. We therefore developed a potent treatment strategy by combining our novel TSHR-CART cells with mitogen-activated protein kinase (MAPK) inhibitors, which redifferentiate thyroid tumors and upregulate TSHR expression. In patient-derived anaplastic thyroid cancer xenografts, combination therapy of TSHR-CART cells and MAPK inhibitors led to increased TSHR expression on the tumor tissue and significantly enhanced antitumor efficacy and prolonged survival compared to TSHR-CART monotherapy. Based on our data, we are launching a phase I clinical trial for TSHR-CART cell therapy alone or in combination with MAPK inhibitors in patients with metastatic thyroid cancers. STATEMENT OF SIGNIFICANCEPoor target selection and antigen escape limit CART cell efficacy in solid tumors. We developed TSHR-CART cells to treat differentiated thyroid cancers but observed TSHR downregulation in dedifferentiated thyroid cancers. We found that MAPK inhibitors restored TSHR expression and sensitized these cancers to TSHR-CART cell therapy.

immunology↗

bioRxiv2024

C-di-AMP accumulation disrupts glutathione metabolism and inhibits virulence program expression in Listeria monocytogenes

C-di-AMP is an essential second messenger in many bacteria but its levels must be regulated. Unregulated c-di-AMP accumulation attenuates the virulence of many bacterial pathogens, including those that do not require c-di-AMP for growth. However, the mechanisms by which c-di-AMP regulates bacterial pathogenesis remain poorly understood. In Listeria monocytogenes, a mutant lacking both c-di-AMP phosphodiesterases, denoted as the {Delta}PDE mutant, accumulates a high c-di-AMP level and is significantly attenuated in the mouse model of systemic infection. All key L. monocytogenes virulence genes are transcriptionally upregulated by the master transcription factor PrfA, which is activated by reduced glutathione (GSH) during infection. Our transcriptomic analysis revealed that the {Delta}PDE mutant is significantly impaired for the expression of virulence genes within the PrfA core regulon. Subsequent quantitative gene expression analyses validated this phenotype both at the basal level and upon PrfA activation by GSH. A constitutively active PrfA* variant, PrfA G145S, which mimics the GSH-bound conformation, restores virulence gene expression in {Delta}PDE but only partially rescues virulence defect. Through GSH quantification and uptake assays, we found that the {Delta}PDE strain is significantly depleted for GSH, and that c-di-AMP inhibits GSH uptake. Constitutive expression of gshF (encoding a GSH synthetase) does not restore GSH levels in the {Delta}PDE strain, suggesting that c-di-AMP inhibits GSH synthesis activity or promotes GSH catabolism. Taken together, our data reveals GSH metabolism as another pathway that is regulated by c-di-AMP. C-di-AMP accumulation depletes cytoplasmic GSH levels within L. monocytogenes that leads to impaired virulence program expression. IMPORTANCEC-di-AMP regulates both bacterial pathogenesis and interactions with the host. Although c-di-AMP is essential in many bacteria, its accumulation also attenuates the virulence of many bacterial pathogens. Therefore, disrupting c-di-AMP homeostasis is a promising antibacterial treatment strategy, and has inspired several studies that screened for chemical inhibitors of c-di-AMP phosphodiesterases. However, the mechanisms by which c-di-AMP accumulation diminishes bacterial pathogenesis are poorly understood. Such understanding will reveal the molecular function of c-di-AMP, and inform therapeutic development strategies. Here, we identify GSH metabolism as a pathway regulated by c-di-AMP that is pertinent to L. monocytogenes replication in the host. Given the role of GSH as a virulence signal, nutrient, and antioxidant, GSH depletion impairs virulence program expression and likely diminishes host adaptation.

microbiology↗

bioRxiv2023

Large-scale phenotypic and genomic characterization of Listeria monocytogenes susceptibility to quaternary ammonium compounds

Listeria monocytogenes is a significant concern for the food industry due to its ability to persist in the food processing environment. Decreased susceptibility to disinfectants is one of the factors that contribute to the persistence of L. monocytogenes. The objective of this study was to explore the diversity of L. monocytogenes susceptibility to quaternary ammonium compounds (QACs) using 1,671 L. monocytogenes isolates. This was used to determine the phenotype-genotype concordance and characterize genomes of the QAC sensitive and tolerant isolates for stress resistance, virulence and plasmid replicon genes. Distribution of QAC tolerance genes among 37,897 publicly available L. monocytogenes genomes were also examined. The minimum inhibitory concentration to QACs was determined by the broth microdilution method and non-sequenced isolates (n=1,244) were whole genome sequenced. Genotype-phenotype concordance was 99% for benzalkonium chloride, DDAC and a commercial QAC based sanitizer. Prevalence of QAC tolerance genes was 23% and 28% in our L. monocytogenes collection and in the global dataset, respectively. qacH was the most prevalent gene in our collection (61%), with 19% prevalence in the global dataset. Notably, bcrABC was most common (72%) globally, while 25% in our collection. Prevalence of emrC and emrE was comparable in both datasets, 7% and 2%, respectively. Replicon genes, indicative of plasmid harborage, were detected in 44% of the isolates and associated with the QAC tolerant phenotype. The presented analysis is based on the biggest L. monocytogenes collection in diversity and quantity for characterization of the L. monocytogenes QAC tolerance at both phenotypic and genomic levels. IMPORTANCEContamination of Listeria monocytogenes within the food processing environment is of concern to the food industry due to challenges in eradicating the pathogen once it becomes persistent in the environment. Genetic markers associated with increased tolerance to disinfectants have been identified, which alongside factors favor the persistence of L. monocytogenes in the production environment. By employing a comprehensive large-scale phenotypic testing and genomic analysis our study significantly enhances the understanding of the prevalence of quaternary ammonium compound (QAC) tolerant L. monocytogenes and the genetic determinants associated with the increased tolerance. Furthermore, we report on the prevalence of QAC tolerance genes among 37,897 publicly available L. monocytogenes sequences and their distribution within clonal complexes, isolation sources and geographical locations. As the propagation of QAC tolerance showed not be evenly distributed globally this highlights that understanding the development of L. monocytogenes disinfectant tolerance can be monitored using publicly available WGS data.

microbiology↗

bioRxiv2023

Stealth liposomes encapsulating a potent ACAT1/SOAT1 inhibitor F12511: pharmacokinetic, biodistribution and toxicity studies in wild-type mice, and efficacy studies in triple transgenic Alzheimer Disease mice.

Cholesterol is essential to cellular function and is stored as cholesteryl esters (CEs). CEs biosynthesis is responsible by the enzymes acyl-CoA: cholesterol acyltransferase 1 and 2 (ACAT1 and ACAT2), with ACAT1 as the primary isoenzyme in most cells in humans. ACATs are targets for atherosclerosis therapies and may also be promising targets for treating Alzheimers Disease (AD). F12511 is a high-affinity ACAT1 inhibitor that has passed phase 1 safety tests for anti-atherosclerosis. Previously, we had developed a nanoparticle system to encapsulate a large concentration of F12511 into a stealth liposome (DSPE-PEG2000 with egg phosphatidylcholine). Here, we injected the nanoparticle encapsulated F12511 (nanoparticle F) intravenously (IV) to wild-type (WT) mice and performed HPLC/MS/MS analysis and ACAT enzyme activity measurement. The results demonstrated that F12511 was present within the mouse brain after a single IV but did not over-accumulate in the brain or other tissues after repeated IVs. Histological examination showed that F12511 did not cause overt neurological or systemic toxicity. We then showed that 2-week IV delivery of nanoparticle F to aging 3xTg AD mice ameliorated amyloidopathy, reduced hyperphosphorylated tau and non-phosphorylated tau, and reduced neuroinflammation. This work lays the foundation with nanoparticle F as a possible therapy for AD and other neurodegenerative diseases.

neuroscience↗

bioRxiv2022

ACAT1/SOAT1 Blockade Suppresses LPS-Mediated Neuroinflammation by Modulating the Fate of Toll-Like Receptor 4 in Microglia

BackgroundCholesterol is essential for growth and maintenance of mammalian cells. It is stored as cholesteryl esters by the enzymes acyl-CoA:cholesterol acyltransferases 1 & 2 (ACAT 1 & 2) (Sterol O-acyltransferase 1 & 2; SOATs in GenBank). ACAT1 blockade (A1B) in macrophages ameliorates various pro-inflammatory responses elicited by lipopolysaccharides (LPS) or by cholesterol loading. In mouse and human brains, Acat1 expression dominates over Acat2 and Acat1 is elevated in many neurodegenerative diseases and in acute neuroinflammation. However, the possible effects of ACAT1 blockade in neuroinflammation, regulated by mediators such as Toll-Like Receptor 4 (TLR4), has not been studied. MethodsWe conducted LPS-induced acute neuroinflammation experiments in control vs myeloid specific or neuron specific Acat1 knockout (KO) mice. Furthermore, we evaluated LPS-induced neuroinflammation in the microglial cell line N9 with or without pre-treatment of the small molecule ACAT1-specific inhibitor K-604. Biochemical and microscopy assays were used to monitor inflammatory responses and the fate of TLR4. ResultsIn vivo studies revealed that Acat1 inactivation in myeloid cell lineage, but not in neurons, markedly attenuated LPS-induced activation of various pro-inflammatory response genes in hippocampus and cortex. Studies in cell culture showed that pre-incubating cells with K-604 significantly ameliorated the pro-inflammatory responses induced by LPS. In cells acutely treated with LPS (for 30 min), pre-incubation with K-604 significantly increased the endocytosis of TLR4, the major transmembrane signaling receptor that mediates LPS-dependent acute neuroinflammation. In cells chronically treated with LPS (for 24-48 hrs), pre-incubation with K-604 significantly decreased the total TLR4 protein content, presumably due to enhanced trafficking of TLR4 to the lysosomes for degradation. For ex vivo evidence, we isolated microglia from adult mice, and found that in mice without LPS stimulation, myeloid Acat1 inactivation altered cellular distribution of TLR4; in mice with LPS stimulation, myeloid Acat1 inactivation decreased the cellular content of TLR4. ConclusionBlocking ACAT1 in mouse microglia alters the fate of TLR4 and suppresses its ability to participate in pro-inflammatory signaling cascade in response to LPS.

neuroscience↗

bioRxiv2021

Listeria monocytogenes GlmR is an accessory uridyltransferase essential for cytosolic survival and virulence

The cytosol of eukaryotic host cells is an intrinsically hostile environment for bacteria. Understanding how cytosolic pathogens adapt to and survive in the cytosol is critical to developing novel therapeutic interventions for these pathogens. The cytosolic pathogen Listeria monocytogenes requires glmR (previously known as yvcK), a gene of unknown function, for resistance to cell wall stress, cytosolic survival, inflammasome avoidance and ultimately virulence in vivo. A genetic suppressor screen revealed that blocking utilization of UDP-GlcNAc by a non-essential wall teichoic acid decoration pathway restored resistance to cell wall stress and partially restored virulence of {Delta}glmR mutants. In parallel, metabolomics revealed that {Delta}glmR mutants are impaired in the production of UDP-GlcNAc, an essential peptidoglycan and wall teichoic acid (WTA) precursor. We next demonstrated that purified GlmR can directly catalyze the synthesis of UDP-GlcNAc from GlcNAc-1P and UTP, suggesting that it is an accessory uridyltransferase. Biochemical analysis of GlmR orthologues suggest that uridyltransferase activity is conserved. Finally, mutational analysis resulting in a GlmR mutant with impaired catalytic activity demonstrated that uridyltransferase activity was essential to facilitate cell wall stress responses and virulence in vivo. Taken together these studies indicate that GlmR is an evolutionary conserved accessory uridyltransferase required for cytosolic survival and virulence of L. monocytogenes. ImportanceBacterial pathogens must adapt to their host environment in order to cause disease. The cytosolic bacterial pathogen Listeria monocytogenes requires a highly conserved protein of unknown function, GlmR (previously known as YvcK) to survive in the host cytosol. GlmR is important for resistance to some cell wall stresses and is essential for virulence. The {Delta}glmR mutant is deficient in production of an essential cell wall metabolite, UDP-GlcNAc, and suppressors which increase metabolite levels also restore virulence. Purified GlmR can directly catalyze the synthesis of UDP-GlcNAc and this enzymatic activity is conserved in pathogens from Firmicutes and Actinobacteria phyla. These results highlight the importance accessory cell wall metabolism enzymes in responding to cell wall stress in a variety of bacterial pathogens.

microbiology↗

bioRxiv2021

NrnA is a linear dinucleotide phosphodiesterase with limited function in cyclic dinucleotide metabolism in Listeria monocytogenes

Listeria monocytogenes produces both c-di-AMP and c-di-GMP to mediate many important cellular processes, but the levels of both nucleotides must be regulated. C-di-AMP accumulation attenuates virulence and diminishes stress response, and c-di-GMP accumulation impairs bacterial motility. An important regulatory mechanism to maintain c-di-AMP and c-di-GMP homeostasis is to hydrolyze them to the linear dinucleotides pApA and pGpG, respectively, but the fates of these hydrolytic products have not been examined in L. monocytogenes. We found that NrnA, a stand-alone DHH-DHHA1 phosphodiesterase, has a broad substrate range, but with a strong preference for linear dinucleotides over cyclic dinucleotides. Although NrnA exhibited detectable cyclic dinucleotide hydrolytic activities in vitro, NrnA had negligible effects on their levels in the bacterial cell, even in the absence of the c-di-AMP phosphodiesterases PdeA and PgpH. The {Delta}nrnA mutant had a mammalian cell infection defect that was fully restored by E. coli Orn. Together, our data indicate that L. monocytogenes NrnA is functionally orthologous to Orn, and its preferred physiological substrates are most likely linear dinucleotides. Furthermore, our findings revealed that, unlike some other c-di-AMP and c-di-GMP-producing bacteria, L. monocytogenes does not employ their hydrolytic products to regulate their phosphodiesterases, at least at the pApA and pGpG levels in the {Delta}nrnA mutant. Finally, the {Delta}nrnA infection defect was overcome by constitutive activation of PrfA, the master virulence regulator, suggesting that accumulated linear dinucleotides might inhibit the expression, stability, or function of PrfA-regulated virulence factors. IMPORTANCEListeria monocytogenes produces both c-di-AMP and c-di-GMP, and encodes specific phosphodiesterases that degrade them into pApA and pGpG, respectively, but the metabolism of these products has not been characterized in this bacterium. We found that L. monocytogenes harbors an NrnA homolog that degrades a broad range of nucleotides, but exhibits a strong biochemical and physiological preference for linear dinucleotides, including pApA and pGpG. Unlike in some other bacteria, these oligoribonucleotides do not appear to interfere with cyclic dinucleotide hydrolysis. The absence of NrnA is well tolerated by L. monocytogenes in broth cultures but impairs its ability to infect mammalian cells. These findings indicate a separation of cyclic dinucleotide signaling and oligoribonucleotide metabolism in L. monocytogenes.

microbiology↗

bioRxiv2021

Limited effects of m6A modification on mRNA partitioning into stress granules

Recent studies have argued that the m6A modification of mRNAs promotes mRNA recruitment to stress granules through the interaction with YTHDF proteins (Anders et al., 2018; Ries et al., 2019). However, mRNAs that contain multiple m6A modified sites partition similarly into stress granules in both wild-type and m6A-deficient cells by single-molecule FISH suggesting m6A modifications play a minor role in mRNA partitioning into stress granules. Moreover, multiple linear regression analysis suggests m6A modification plays a minimal role in stress granule recruitment. Finally, the artificial tethering of 25 YTHDF proteins on reporter mRNAs leads to only a modest increase in mRNA partitioning to stress granules. These results indicate m6A modification makes a small, but measurable, contribution to recruiting specific mRNAs to stress granules.

molecular biology↗

bioRxiv2020

RNA partitioning into stress granules is based on the summation of multiple interactions

Stress granules (SGs) are stress-induced RNA-protein assemblies formed from a complex transcriptome of untranslating ribonucleoproteins (RNPs). Although RNAs can be either enriched or depleted from SGs, the rules that dictate RNA partitioning into SGs are unknown. We demonstrate that the SG-enriched NORAD RNA is sufficient to enrich a reporter RNA within SGs through the combined effects of multiple elements. Moreover, artificial tethering of G3BP1 or TIA1 can target mRNAs into SGs in a dose-dependent manner that suggests individual protein interactions have small effects on the SG partitioning of mRNPs, which is supported by the observation that the SG transcriptome is largely unchanged in cell lines lacking the abundant SG RNA-binding proteins G3BP1 and G3BP2. We suggest the targeting of RNPs into SGs is due to a summation of potential RNA-protein, protein-protein, and RNA-RNA interactions with no single interaction dominating RNP recruitment into SGs.

molecular biology↗

bioRxiv2018

Polycomb Cbx2 Condensates Assemble through Phase Separation

Polycomb group (PcG) proteins are master regulators of development and differentiation. Mutation and dysregulation of PcG genes cause developmental defects and cancer. PcG proteins form condensates in the nucleus of cells and these condensates are the physical sites of PcG-targeted gene silencing. However, the physiochemical principles underlying the PcG condensate formation remain unknown. Here we show that Polycomb repressive complex 1 (PRC1) protein Cbx2, one member of the Cbx family proteins, contains a long stretch of intrinsically disordered region (IDR). Cbx2 undergoes phase separation to form condensates. Cbx2 condensates exhibit liquid-like properties and can concentrate DNA and nucleosomes. We demonstrate that the conserved residues within the IDR promote the condensate formation in vitro and in vivo. We further indicate that H3K27me3 has minimal effects on the Cbx2 condensate formation while depletion of core PRC1 subunits facilitates the condensate formation. Thus, our results reveal that PcG condensates assemble through liquid-liquid phase separation (LLPS) and suggest that PcG-bound chromatin is in part organized through phase-separated condensates.

biochemistry↗