Nucleobase deaminases: a potential enzyme system for new therapies

Escherichia coli cytosine deaminase: Structural and biotechnological aspects

Suicide gene therapy involves introducing viral or bacterial genes into tumor cells, which enables the conversion of a nontoxic prodrug into a toxic-lethal drug. The application of the bacterial cytosine deaminase (bCD)/5-fluorocytosine (5-FC) approach has been beneficial and progressive within the current field of cancer therapy because of the enhanced bystander effect. The basis of this method is the preferential deamination of 5-FC to 5-fluorouracil by cancer cells expressing cytosine deaminase (CD), which strongly inhibits DNA synthesis and RNA function, effectively targeting tumor cells. However, the poor binding affinity of toward 5-FC compared to the natural substrate cytosine and/or inappropriate thermostability limits the clinical applications of this gene therapy approach. Nowadays, many genetic engineering studies have been carried out to solve and improve the activity of this enzyme. In the current review, we intend to discuss the biotechnological aspects of Escherichia coli CD, including its structure, functions, molecular cloning, and protein engineering. We will also explore its relevance in cancer clinical trials. By examining these aspects, we hope to provide a thorough understanding of E. coli CD and its potential applications in cancer therapy.

Modern Approaches to the Genome Editing of Antibiotic Biosynthetic Clusters in Actinomycetes

Representatives of the phylum Actinomycetota are one of the main sources of secondary metabolites, including antibiotics of various classes. Modern studies using high-throughput sequencing techniques enable the detection of dozens of potential antibiotic biosynthetic genome clusters in many actinomycetes; however, under laboratory conditions, production of secondary metabolites amounts to less than 5% of the total coding potential of producer strains. However, many of these antibiotics have already been described. There is a continuous "rediscovery" of known antibiotics, and new molecules become almost invisible against the general background. The established approaches aimed at increasing the production of novel antibiotics include: selection of optimal cultivation conditions by modifying the composition of nutrient media; co-cultivation methods; microfluidics, and the use of various transcription factors to activate silent genes. Unfortunately, these tools are non-universal for various actinomycete strains, stochastic in nature, and therefore do not always lead to success. The use of genetic engineering technologies is much more efficient, because they allow for a directed and controlled change in the production of target metabolites. One example of such technologies is mutagenesis-based genome editing of antibiotic biosynthetic clusters. This targeted approach allows one to alter gene expression, suppressing the production of previously characterized molecules, and thereby promoting the synthesis of other unknown antibiotic variants. In addition, mutagenesis techniques can be successfully applied both to new producer strains and to the genes of known isolates to identify new compounds.

Hydrolysis of Acetamide on Low-Index CeO2 Surfaces: Ceria as a Deamidation and General De-esterification Catalyst

Using DFT calculations and acetamide as the main example, we show that ceria is a potential catalyst for the hydrolysis of amide and similar bonds. The overall reaction is endergonic in the gas phase, yielding acetic acid and ammonia, but is slightly exergonic in the aqueous phase, which facilitates ionization of the products (CH₃COO^– and NH₄⁺). Neighboring Ce and O sites on the CeO₂(111), (110), and (100) facets are conducive to the formation of an activated metastable tetrahedral intermediate (TI) complex, followed by C–N bond scission. With van der Waals and solvation effects taken into account, the overall reaction energetics is found to be most favorable on the (111) facet as desorption of acetic acid is much more uphill energetically on (110) and (100). We further suggest that the Ce–O–Ce sites on ceria surfaces can activate X(=Y)–Z type bonds in amides, amidines, and carboxylate and phosphate esters, among many others that we term “generalized esters”. A Brønsted-Evans–Polanyi relationship is identified correlating the stability of the transition and final states of the X–Z generalized ester bond scission. A simple descriptor (ΣΔχ) based on the electronegativity of the atoms that constitute the bond (X, Y, Z) versus those of the catalytic site (O, Ce, Ce) captures the trend in the stability of the transition state of generalized ester bond scission and suggests a direction for modifying ceria for targeting specific organic substrates.

Trehalose supplementation enhanced the biocontrol efficiency of Sporidiobolus pararoseus Y16 through increased oxidative stress tolerance and altered transcriptome

BACKGROUND

In the process of biological control, the antagonistic yeasts contend with various stresses that negatively influence yeasts' biocontrol efficiency. In the current study, we investigated the effect of trehalose supplementation on the biocontrol efficiency and oxidative stress tolerance of Sporidiobolus pararoseus Y16.

RESULTS

S. pararoseus Y16, an antagonistic yeast cultured in trehalose supplemented medium, exhibited better biocontrol efficiency against Penicillium expansum and Aspergillus tubingensis in table grapes. Trehalose-treated S. pararoseus Y16 cells showed good proliferation efficiency and oxidative stress tolerance than untreated cells. Increased β-1,3-glucanase, catalase, superoxide dismutase activity, and low protein carbonylation were observed in trehalose-amended S. pararoseus Y16 upon H₂ O₂ exposure. The RNA sequencing results indicated that trehalose significantly altered the transcriptome of S. pararoseus Y16. The GO, KEGG, and COG annotations revealed that the differentially regulated genes corresponded to the various biological process of the yeast.

CONCLUSION

Our findings suggested that trehalose use could enhance the biocontrol efficiency and oxidative stress tolerance of S. pararoseus Y16. Trehalose supplementation altered the transcriptome of S. pararoseus Y16, particularly the genes that correspond to amino acid metabolism, nucleotide metabolism, and protein modification. Thereby the oxidative stress tolerance and biological control efficiency of S. pararoseus Y16 was enhanced by trehalose. © 2021 Society of Chemical Industry.

Insights into the Dual Shuttle Catalytic Mechanism of Guanine Deaminase

Guanine deaminases (GD) are essential enzymes that help in regulating the nucleobase pool. Since the deamination reaction can result in the accumulation of mutagenic bases that can lead to genomic instability, these enzymes are tightly regulated and are nonpromiscuous. Here, we delineate the basis of their substrate fidelity via entailing the reaction mechanism of deamination by employing density functional theory (DFT) calculations on NE0047, a GD from Nitrosomonas europaea. The results show that, unlike pyrimidine deaminases, which require a single glutamic acid as a proton shuttle, GDs involve two amino acids, E79 and E143 (numbering in NE0047), which control its reactivity. The hybrid quantum mechanics/molecular mechanics (QM/MM) calculations have shown that the first Zn-bound proton transfer to the N3 atom of the substrate is mediated by the E79 residue, and the second proton is transferred to the amine nitrogen of substrate via E143. Moreover, cluster models reveal that the crystallographic water molecules near the active site control the reactivity. A comparison with human GD reveals that the proposed catalytic mechanism is generic, and the knowledge generated here can be effectively applied to design selective inhibitors.

Real-Time Monitoring of Human Guanine Deaminase Activity by an Emissive Guanine Analog

Guanine deaminase (GDA) deaminates guanine to xanthine. Despite its significance, the study of human GDA remains limited compared to other metabolic deaminases. As a result, its substrate and inhibitor repertoire are limited, and effective real-time activity, inhibitory, and discovery assays are missing. Herein, we explore two emissive heterocyclic cores, based on thieno[3,4-d]pyrimidine (^thN) and isothiazole[4,3-d]pyrimidine (^tzN), as surrogate GDA substrates. We demonstrate that, unlike the thieno analog, ^thG_N, the isothiazolo guanine surrogate, ^tzG_N, does undergo effective enzymatic deamination by GDA and yields the spectroscopically distinct xanthine analog, ^tzX_N. Further, we showcase the potential of this fluorescent nucleobase surrogate to provide a visible spectral window for a real-time study of GDA and its inhibition.

Structure guided mutagenesis reveals the substrate determinants of guanine deaminase

Guanine deaminases (GDs) are essential enzymes that regulate the overall nucleobase pool. Since the deamination of guanine to xanthine results in the production of a mutagenic base, these enzymes have evolved to be very specific in nature. Surprisingly, they accept structurally distinct triazine ammeline, an intermediate in the melamine pathway, as one of the moonlighting substrates. Here, by employing NE0047 (a GD from Nitrosomonas europaea), we delineate the nuance in the catalytic mechanism that allows these two distinct substrates to be catalyzed. A combination of enzyme kinetics, X-ray crystallographic, and calorimetric studies reveal that GDs operate via a dual proton shuttle mechanism with two glutamates, E79 and E143, crucial for deamination. Additionally, N66 appears to be central for substrate anchoring and participates in catalysis. The study highlights the importance of closure of the catalytic loop and of maintenance of the hydrophobic core by capping residues like F141 and F48 for the creation of an apt environment for activation of the zinc-assisted catalysis. This study also analyzes evolutionarily distinct GDs and asserts that GDs incorporate subtle variations in the active site architectures while keeping the most critical active site determinants conserved.

Integrated computational approach toward discovery of multi-targeted natural products from Thumbai (Leucas aspera) for attuning NKT cells

A multi-omics-based approach targeting the plant-based natural products from Thumbai (Leucas aspera), an important yet untapped potential source of many therapeutic agents for myriads of immunological conditions and genetic disorders, was conceptualized to reconnoiter its potential biomedical application. A library of 79 compounds from this plant was created, out of which 9 compounds qualified the pharmacokinetics parameters. Reverse pharmacophore technique for target fishing of the screened compounds was executed through which renin receptor (ATP6AP2) and thymidylate kinase (DTYMK) were identified as potential targets. Network biology approaches were used to comprehend and validate the functional, biochemical and clinical relevance of the targets. The target-ligand interaction and subsequent stability parameters at molecular scale were investigated using multiple strategies including molecular modeling, pharmacophore approaches and molecular dynamics simulation. Herein, isololiolide and 4-hydroxy-2-methoxycinnamaldehyde were substantiated as the lead molecules exhibiting comparatively the best binding affinity against the two putative protein targets. These natural lead products from L. aspera and the combinatorial effects may have plausible medical applications in a wide variety of neurodegenerative, genetic and developmental disorders. The lead molecules also exhibit promising alternative in diagnostics and therapeutics through immuno-modulation targeting natural killer T-cell function in transplantation-related pathogenesis, autoimmune and other immunological disorders.Communicated by Ramaswamy H. Sarma.

Discovery of Bacterial Deaminases That Convert 5-Fluoroisocytosine Into 5-Fluorouracil

Cytosine is one of the four letters of a standard genetic code, found both in DNA and in RNA. This heterocyclic base can be converted into uracil upon the action of the well-known cytosine deaminase. Isocytosine (2-aminouracil) is an isomer of cytosine, yet the enzymes that could convert it into uracil were previously mainly overlooked. In order to search for the isocytosine deaminases we used a selection strategy that is based on uracil auxotrophy and the metagenomic libraries, which provide a random pool of genes from uncultivated soil bacteria. Several genes that encode isocytosine deaminases were found and two respective recombinant proteins were purified. It was established that both novel deaminases do not use cytosine as a substrate. Instead, these enzymes are able to convert not only isocytosine into uracil, but also 5-fluoroisocytosine into 5-fluorouracil. Our findings suggest that novel isocytosine deaminases have a potential to be efficiently used in targeted cancer therapy instead of the classical cytosine deaminases. Use of isocytosine instead of cytosine would produce fewer side effects since deaminases produced by the commensal E. coli gut flora are ten times less efficient in degrading isocytosine than cytosine. In addition, there are no known homologs of isocytosine deaminases in human cells that would induce the toxicity when 5-fluoroisocytosine would be used as a prodrug.