Favipiravir strikes the SARS-CoV-2 at its Achilles heel, the RNA polymerase

The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. Here we show that Favipiravir exerts an antiviral effect as a nucleotide analogue through a combination of chain termination, slowed RNA synthesis and lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19.

A61 Large RNA genomes: Is RNA polymerase fidelity enough?

Large-genome Nidoviruses and Nidovirus-like viruses reside at the current boundary of largest RNA genome sizes. They code for an unusually large number of gene products matching that of small DNA viruses (e.g. DNA bacteriophages). The order of appearance and distribution of enzyme genes along various virus families (e.g. helicase and ExoN) may be seen as an evolutionary marker in these large RNA genomes lying at the genome size boundary. A positive correlation exists between (+)RNA virus genome sizes and the presence of the RNA helicase and the ExoN domains. Although the mechanistic basis of the presence of the helicase is still unclear, the role of the ExoN activity has been linked to the existence of an RNA synthesis proofreading system. In large Nidovirales, ExoN is bound to a processive replicative RNA-dependent RNA polymerase (RdRp) and corrects mismatched bases during viral RNA synthesis. Over the last decade, a view of the overall process has been refined in Coronaviruses, and in particular in our lab (Ferron et al., PNAS, 2018). We have identified genetic markers of large RNA genomes that we wish to use to data-mine currently existing metagenomic datasets. We have also initiated a collaboration to sequence and explore new viromes that will be searched according to these criteria. Likewise, we have a collection of purified viral RdRps that are currently being used to generate RNA synthesis products that will be compared to existing NGS datasets of cognate viruses. We will be able to have an idea about how much genetic diversity is possibly achievable by viral RdRp (‘tunable fidelity’) versus the detectable diversity (i.e. after selection in the infected cell) that is actually produced.

SPINE bioinformatics and data-management aspects of high-throughput structural biology

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high‐throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high‐throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high‐throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

Histochemical method for characterization of enzyme crystals: application to crystals of Torpedo californica acetylcholinesterase

Histochemical methods are employed to detect and localize a wide range of enzymes. Even though protein crystallographers do not commonly use this technique, the extensively used colorimetric reaction of Karnovsky was successfully adapted for easy and quick identification of acetylcholinesterase crystals. The method relies on the reduction of ferricyanide to ferrocyanide by thiocholine, released from acetylthiocholine by enzymatic hydrolysis, followed by formation of a cupric ferrocyanide precipitate, and allows rapid differentiation between salt and enzyme crystals and between native and inhibited crystals of the enzyme.

Serum leptin concentrations in patients with anorexia nervosa, bulimia nervosa and non-specific eating disorders correlate with the body mass index but are independent of the respective disease

OBJECTIVE

Leptin, the product of the ob gene, is a recently discovered hormone secreted by adipocytes. Serum leptin concentrations increase in correlation with the percentage of body fat, but little else is known about the physiological actions of leptin in humans. The aim of this study was to determine the role of leptin in severe eating disorders, and whether its levels are correlated with the specific disease or exclusively with body weight.

TESTS

Serum concentrations of human leptin were analysed by specific radioimmunoassay and compared with the individual body mass indexes (BMI). The correlations between serum leptin concentrations and BMI, age and height were analysed.

PATIENTS

A total of 65 women were studied: 25 patients with anorexia nervosa, 20 women with bulimia nervosa, 6 women with a diagnosis of nonspecific eating disorder, and 14 normal-weight women who acted as controls. At the time of the study, the patients were non-cured, under treatment, and at different stages of therapeutic evolution.

MEASUREMENTS

Plasma leptin levels were measured by specific radioimmunoassay.

RESULTS

The mean serum leptin in the normal-weight women was 10.5 +/- 1.1 micrograms/l, compared with 7.6 +/- 1.1 micrograms/l in the anorexia nervosa patients (P < 0.05). This reduction in leptin levels was paralleled by the differences in BMI (21.4 +/- 0.4 vs 18.8 +/- 0.2) P < 0.05. These differences between the controls and anorexia nervosa patients were not observed in patients with bulimia nervosa who had a mean serum leptin level of 9.9 +/- 1.4 micrograms/l and BMI of 21.3 +/- 0.6, neither significantly different from controls. On the contrary, patients with non-specific eating disorders showed a large reduction in BMI (17.9 +/- 1.2, P < 0.05 vs control), and a parallel reduction in serum leptin levels, 4.5 +/- 1.0 (P < 0.05 vs controls). When individual values of leptin were plotted against BMI a wide range was observed in all groups; in the control subjects from 5.6 to 17.7 micrograms/l, in anorexia nervosa patients from 2.1 to 28.1 micrograms/l, in patients with bulimia nervosa between 2.6 and 25.9 micrograms/l, and in women with non-specific eating disorder from 2.0 to 8.9. No correlation was observed with the specific disease but in each group a significant correlation was observed only with BMI.

CONCLUSIONS

Serum leptin levels in three groups of patients affected by severe eating disorders are not related to the specific pathology but are correlated with the individual BMI. The analysis of leptin values may be a useful index of assessing the adipose tissue stores in the clinical setting, but will be of no help for diagnosis nor prognosis of severe eating disorders.

Metabolization of elemental sulfur in wheat leaves consecutive to its foliar application

The qualitative and quantitative aspects of elemental sulfur metabolization in wheat leaves and its effect upon photosynthetic metabolism were studied through the application of micronized sulfur upon the third leaf. Energy-dispersive x-ray analysis combined with scanning electron microscopy emphasized the existence of a sulfur peak associated with a strong potassium peak in the spectra of different tissue regions for treated leaves only, supplying an original evidence of sulfur uptake. Experiments with(35)S-labeled micronized sulfur showed that about 2% of the labeled S was absorbed and metabolized into cystine, methionine, glutathione, and sulfate. The close correlation between the excess of oxygen uptake and oxygen needs for sulfur oxidation in conjunction with the absence of hydrogen sulfide released by treated leaves support direct and fast oxidation of sulfur into sulfate according to a pathway still unclear but independent of photosynthetic CO(2) metabolism in treated leaf. The mechanisms involved in the primary metabolism of element sulfur in wheat therefore appear to be different from those in fungi.

High CO2 partial pressure effects on dark and light CO2 fixation and metabolism in Vicia faba leaves

Stomatal opening on Vicia faba can be induced by high CO2 partial pressures (10.2%) in dark as well as in light. Stomatal aperture was measured in both cases with a hydrogen porometer. The distribution of (14)C among early products of photosynthesis was studied. Comparisons are made with carboxylations occurring when stomata were open in the dark with CO2-free air and in light with 0.034% CO2. Results showed that in high CO2 partial pressure in light, less radioactivity was incorporated in Calvin cycle intermediates and more in sucrose. β carboxylations and photorespiration seemed to be inhibited. In the dark in both CO2 conditions, (14)C incorporation was found in malate and aspartate but also in serine and glycerate in high CO2 conditions. In light these changes in metabolic pathways may be related with the deleterious effects recorded on leaves after long-term expositions to high partial pressure of CO2.