Flux Balance Analysis Reveals Potential Anti-HIV-1 Metabolic Targets

Background:Human immunodeficiency virus type 1(HIV-1)remains a persistent global health challenge.Therefore,a continuous exploration of novel therapeutic strategies is essential.A comprehensive understanding of how HIV-1 utilizes the cellular metabolism machinery for replication can provide insights into new therapeutic approaches.Methods:In this study,we performed a flux balance analysis using a genome-scale metabolic model(GEM)integrated with an HIV-1 viral biomass objective function to identify potential targets for anti–HIV-1 interventions.We generated a GEM by integrating an HIV-1 production reaction into CD4+T cells and optimized for both host and virus optimal states as objective functions to depict metabolic profiles of cells in the status for optimal host biomass maintenance or for optimal HIV-1 virion production.Differential analysis was used to predict biochemical reactions altered optimal for HIV-1 production.In addition,we conducted in silico simulations involving gene and reaction knock-outs to identify potential anti–HIV-1 targets,which were subsequently validated by human phytohemagglutinin(PHA)blasts infected with HIV-1.Results:Differential analysis identified several altered biochemical reactions,including increased lysine uptake and oxidative phosphorylation(OXPHOS)activities in the virus optima compared with the host optima.In silico gene and reaction knock-out simulations revealed de novo pyrimidine synthesis,and OXPHOS could serve as potential anti–HIV-1 metabolic targets.In vitro assay confirmed that targeting OXPHOS using metformin could suppress the replication of HIV-1 by 56.6%(385.4±67.5 pg/mL in the metformintreated group vs.888.4±32.3 pg/mL in the control group,P<0.001).Conclusion:Our integrated host-virus genome-scale metabolic study provides insights on potential targets(OXPHOS)for anti-HIV therapies.

Recent advances in the biosynthesis of coumarin and its derivatives

Coumarin and its derivatives,presenting in many organisms(plants,fungi,and bacteria),are critical metabolites composed of fused benzene andα-pyrone rings.With unique biological and chemical properties,coumarin derivatives possess great technological potential in the agrochemicals,pharmaceuticals,food,and cosmetic industries.The increasing demand for coumarin derivatives accelerates the research in biological and chemical synthesis to provide stable and scalable sources of coumarins.However,the complex structures and unknown pathways have limited the progress in the biosynthesis of coumarin derivatives.Here,we summarize recent developments and provide a detailed analysis of coumarin derivative biosynthetic pathways in different organisms.

Fundamental CRISPR-Cas9 tools and current applications in microbial systems

Derived from the bacterial adaptive immune system,CRISPR technology has revolutionized conventional genetic engineering methods and unprecedentedly facilitated strain engineering.In this review,we outline the fundamental CRISPR tools that have been employed for strain optimization.These tools include CRISPR editing,CRISPR interference,CRISPR activation and protein imaging.To further characterize the CRISPR technology,we present current applications of these tools in microbial systems,including model-and non-model industrial microorganisms.Specially,we point out the major challenges of the CRISPR tools when utilized for multiplex genome editing and sophisticated expression regulation.To address these challenges,we came up with strategies that place emphasis on the amelioration of DNA repair efficiency through CRISPR-Cas9-assisted recombineering.Lastly,multiple promising research directions were proposed,mainly focusing on CRISPR-based construction of microbial ecosystems toward high production of desired chemicals.

Observations of abundant structural and electronic phases in potassium-doped single-layer p-quaterphenyl film

Scanning tunneling microscopy/spectroscopy is applied herein to study the pristine and potassium(K)-doped single-layer pquaterphenyl(P4P) films grown on the Au(111) substrate at the molecular level. Abundant complex structural and electronic phases are induced by various K doping. The Fermi-level pinning effect is observed at a low doping level. On the contrary,K3P4P exhibits intriguing versatile phases and properties because charge carriers are effectively doped in. For example, two kinds of molecular vibration modes with energies below 100 meV are observed, indicating a possible strong electron-phonon coupling. The splitting of the lowest unoccupied molecular orbital state in K3P4P illustrates an electronic correlation effect, and its strength varies for four different K3P4P phases with different structures. In addition, the appearance of a Kondo resonance on the molecular vacancy/impurity implies a local molecular magnetic moment. Our results demonstrate that the complex electronic properties of an alkali metal-doped P4P/Au film stem from the existence of many competing interactions, such as electronelectron correlations and electron-vibration coupling, which can be effectively tuned via variable carrier doping and molecular structure. Our work also opens new routes toward engineering novel molecular devices and creating new electronic phases in strongly correlated molecular materials.

Two-impurity Kondo effect in potassium-doped single-layer p-sexiphenyl films

Herein, we show that a self-assembled phase of potassium(K)-doped single-layer para-sexiphenyl(PSP) film on a gold substrate is an excellent platform for studying the two-impurity Kondo model. On K-doped PSP molecules well separated from others, we observe a Kondo resonance peak close to EFwith a Kondo temperature of 30 K. The Kondo resonance peak splits when another K-doped PSP molecule is present in the vicinity, and the splitting gradually increases with the decrease in intermolecular distance without signs of phase transition. Our data demonstrate how a Kondo singlet state gradually evolves into an antiferromagnetic singlet state due to the competition between Kondo screening and antiferromagnetic Ruderman-Kittel-Kasuya-Yosida coupling,as described in the two-impurity Kondo model. Intriguingly, the antiferromagnetic singlet is quickly destroyed on increasing temperature and transforms back to a Kondo singlet below the Kondo temperature. Our data provide a comprehensive picture and quantitative constraints on related theories and calculations of the two-impurity Kondo model.