Communication and Cross-Regulation Between Multiple Concatenated Enzymatic Reaction Networks

Nature connects multiple fuel-driven chemical/enzymatic reaction networks (CRNs/ERNs) via cross-regulation to hierarchically control biofunctions for a tailored adaption in complex sensory landscapes. In contrast, emerging artificial fuel-driven systems most-ly focus on a single CRN and their implementation to direct self-assembly or material responses. In this work, we introduce a facile example of communication and cross-regulation among multiple DNA-based ERNs regulated by a concatenated RNA transcription regulator. For this purpose, we run two fuel-driven DNA-based ERNs by concurrent NAD+-fueled ligation and restriction via endo-nucleases (REases) in parallel. ERN one allows for the dynamic steady-state formation of the promoter sequence for T7 RNA poly-merase, which activates RNA transcription. The produced RNA regulator can repress or promote the second ERN via RNA-mediated strand displacement. Furthermore, adding RNase H to degrade the produced RNA can restart the reaction or tune the lag time of two ERNs, giving rise to a repression-recovery and promotion-stop processes. We believe that concatenation of multiple CRNs provides a basis for the design of more elaborate autonomous regulatory mechanisms in systems chemistry and synthetic biology.

Synergistic Interferon-Alpha-Based Combinations for Treatment of SARS-CoV-2 and Other Viral Infections

Background: There is an urgent need for new antivirals with powerful therapeutic potential and tolerable side effects. Methods: Here, we tested the antiviral properties of interferons (IFNs), alone and with other drugs in vitro. Results: While IFNs alone were insufficient to completely abolish replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), IFNα, in combination with remdesivir, EIDD-2801, camostat, cycloheximide, or convalescent serum, proved to be more effective. Transcriptome and metabolomic analyses revealed that the IFNα–remdesivir combination suppressed SARS-CoV-2-mediated changes in Calu-3 cells and lung organoids, although it altered the homeostasis of uninfected cells and organoids. We also demonstrated that IFNα combinations with sofosbuvir, telaprevir, NITD008, ribavirin, pimodivir, or lamivudine were effective against HCV, HEV, FLuAV, or HIV at lower concentrations, compared to monotherapies. Conclusions: Altogether, our results indicated that IFNα can be combined with drugs that affect viral RNA transcription, protein synthesis, and processing to make synergistic combinations that can be attractive targets for further pre-clinical and clinical development against emerging and re-emerging viral infections.

Theoretical analysis of RNA polymerase fidelity: a steady-state copolymerization approach

The fidelity of DNA transcription catalyzed by RNA polymerase (RNAP) has long been an important issue in biology. Experiments have revealed that RNAP can incorporate matched nucleotides selectively and proofread the incorporated mismatched nucleotides. However, systematic theoretical researches on RNAP fidelity are still lacking. In the last decade, several theories on RNA transcription have been proposed, but they only handled highly simplified models without considering the high-order neighbor effects and the oligonucleotides cleavage both of which are critical for the overall fidelity. In this paper, we regard RNA transcription as a binary copolymerization process and calculate the transcription fidelity by the steady-state copolymerization theory recently proposed by us for DNA replication. With this theory, the more realistic models considering higher-order neighbor effects, oligonucleotides cleavage, multi-step incorporation and multi-step cleavage can be rigorously handled.

Extracellular vesicle therapeutics: the issue of one size fits all

Extracellular vesicles (EV) are mediators of intercellular communication locally in tissue microenvironments and enable distal across organ communication between cells of the same origin and those from different sources. EV surface proteins and lipids enable interaction with particular cells, whereas their internal payload of RNA, transcription factors, DNA, enzymes and metabolites functionally alters recipient cells. EV-interactions and uptake induce changes in cellular proliferation, differentiation, cell movement, as well as transcriptional and epigenetic regulation. These unique properties of EV poise them as attractive therapeutics in a broad range of pathologies, but questions remain in translating EV discoveries to effective therapies. Here, I briefly discuss the need for more stringent considerations for EV-therapeutic effects with a focus on EV biodistribution profiles in appropriate disease models and routes of EV administration with a particular focus on the vasculature.

Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins

Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious particle, limits understanding of molecular interactions among proteins and RNA, and their contributions to virion assembly and RNA transcription. Here, we report the 3.3 Å-resolution asymmetric reconstruction of transcribing MRV and in situ atomic models of its capsid proteins, the asymmetrically attached RNA-dependent RNA polymerase (RdRp) λ3, and RdRp-bound nucleoside triphosphatase μ2 with a unique RNA-binding domain. We reveal molecular interactions among virion proteins and genomic and messenger RNA. Polymerase complexes in three Spinoreovirinae subfamily members are organized with different pseudo-D3d symmetries to engage their highly diversified genomes. The above interactions and those between symmetry-mismatched receptor-binding σ1 trimers and RNA-capping λ2 pentamers balance competing needs of capsid assembly, external protein removal, and allosteric triggering of endogenous RNA transcription, before, during and after infection, respectively.

Interactions between m6A modification and miRNAs in malignant tumors

Recently, the regulatory role of epigenetic modifications in the occurrence and development of malignant tumors has attracted extensive attention. RNA m6A methylation is the most abundant RNA modification in eukaryotic cells and regulates RNA transcription, processing, splicing, degradation, and translation. As important biomarkers, miRNAs play a crucial role in the diagnosis and treatment of diseases as well as in the development of anti-tumor drugs. Recently, increasing evidence has shown that m6A modification plays a vital role in regulating miRNA biosynthesis. We, herein, have reviewed the enzyme system involved in m6A methylation and the crosstalk between m6A modification and miRNAs in cancer. In addition, we have discussed the potential clinical applications and possible development directions of this field in the future.

Compared to liver, bile duct and skeletal muscle garlic (versus normal saline) only enhances pancreas insulin m-RNA transcription that corresponds to islets cellular plasticity and local and circulating hyperinsulinemia in diabetic rats

Background: Garlic aqueous extract (GE) augments insulin circulating concentration in streptozotocin-induced type-1 diabetes mellitus (STZ-DM) rat model. Objective: This study investigated at 4 stages in a time-line fashion whether modifications in insulin m-RNA transcription occur, and if they do, are they related to accumulative changes in insulin - serum and tissue concentrations and immunohistochemical (IHC) localizations and plasticities as part of the GE-induced insulinogenic mechanism(s) in the pancreas, liver, bile duct and gastrocnemius skeletal muscle (GSM) of STZ-DM rats. Method: The body weight, food and water intake, urine output, fasting blood glucose (FBG), serum insulin (SI), in addition to tissues insulin concentrations, IHC localizations and numerical intensities and m-RNA transcriptions were investigated before (basal level = BL) and after 1, 4 and 8 weeks of oral treatment in normal rats given normal saline (NR-NS), diabetic rats given normal saline (DR-NS) and diabetic rats given GE (DR-GE). The readings collected were compared using two-way ANOVA with LSD post-hoc test (IBM SPSS - V.22) and differences were considered significant when P <0.05.Results: Compared to NR-NS, DR-NS showed typical diabetic biophysical symptoms in addition to significant accumulative increases in FBG and reductions in SI, which corresponded positively with reductions in pancreatic insulin IHC localization and numerical intensity and m-RNA transcription. Conversely, and in comparison to DR-NS, DR-GE showed amelioration of diabetic biophysical symptoms, in addition to significant accumulative decreases in FBG and increases in SI, which corresponded positively with increases in pancreatic insulin IHC localization and numerical intensity and m-RNA transcription. The liver, bile duct and GSM did not show any changes in the targeted parameters (or indicators of insulin synthesis: proinsulin or C-peptide) in response to GE treatment. Conclusion: GE induced increases in circulating insulin concentration could have been due to increases in pancreas insulin concentrations as a result of an enhancement in islets cellular plasticity and m-RNA transcription. Accordingly, garlic insulinogenic action could be partly due to modification of pancreas genetic expression.

FUS/TLS suppresses enterovirus replication and promotes antiviral innate immune responses

During viral infection, the dynamic virus-host relationship is constantly in play. Many cellular proteins such as RNA-binding proteins (RBPs) have been shown to mediate antiviral responses during viral infection. Here we reported that the RBP, fused in sarcoma/translocated in liposarcoma (FUS/TLS), acts as a host restricting factor against the infection of coxsackievirus B3 (CVB3). Mechanistically, we found that deletion of FUS leads to increased viral RNA transcription and enhanced internal ribosome entry site (IRES)-driven translation, with no apparent impact on viral RNA stability. We further demonstrated that FUS physically interacts with viral genome, which may contribute to direct inhibition of viral RNA transcription/translation. Moreover, we identified a novel function for FUS in regulating host innate immune response. We showed that in the absence of FUS, gene expression of type I interferons and proinflammatory cytokines elicited by viral or bacterial infection is significantly impaired. Emerging evidence suggests a role for stress granules (SGs) in antiviral innate immunity. We further uncovered that knockout of FUS abolishes the ability to form SGs upon CVB3 infection or polyinosinic:polycytidylic acid (polyIC) treatment. Finally, we showed that, to avoid FUS-mediated antiviral response and innate immunity, CVB3 infection results in cytoplasmic mislocalization and cleavage of FUS through the enzymatic activity of viral proteases. Together, our findings in this study identified FUS as a novel host antiviral factor, which restricts CVB3 replication through direct inhibition of viral RNA transcription and protein translation and by regulating host antiviral innate immunity. IMPORTANCE Enteroviruses are common human pathogens, including those that cause myocarditis (coxsackievirus B3, CVB3), poliomyelitis (poliovirus) and hand, foot and mouse disease (enterovirus 71). Understanding the virus-host interaction is crucial for finding the treatment and prevention of these pathogens. In this study, we explored the interplay between host RNA binding protein FUS/TLS and CVB3 and reported that FUS/TLS restricts CVB3 replication through direct inhibition of viral RNA transcription/translation and by regulation of cellular antiviral innate immunity. To impede the antiviral role of FUS, CVB3 targets FUS for mislocalization and cleavage. Findings from this study provide novel insights into interactions between CVB3 and the FUS, which may lead to novel therapeutic interventions against enterovirus-induced diseases.