Emerging WuHan (COVID-19) coronavirus:glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26

The recent outbreak of pneumonia-causing COVID-19 in China is an urgent global public health issue with an increase in mortality and morbidity. Here we report our modelled homo-trimer structure of COVID-19 spike glycoprotein in both closed (ligand-free) and open (ligand-bound) conformation, which is involved in host cell adhesion. We also predict the unique N- and O-linked glycosylation sites of spike glycoprotein that distinguish it from the SARS and underlines shielding and camouflage of COVID-19 from the host the defence system. Furthermore, our study also highlights the key finding that the S1 domain of COVID-19 spike glycoprotein potentially interacts with the human CD26, a key immunoregulatory factor for hijacking and virulence. These findings accentuate the unique features of COVID-19 and assist in the development of new therapeutics

Structural Insights into SARS-CoV‑2 Nonstructural Protein 1 Interaction with Human Cyclophilin and FKBP1 to Regulate Interferon Production

The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 coronavirus and the perpetual rise of new variants warrant investigation of the molecular and structural details of the infection process and modulation of the host defense by viral proteins. This Letter reports the combined experimental and computational approaches to provide key insights into the structural and functional basis of Nsp1’s association with different cyclophilins and FKBPs in regulating COVID-19 infection. We demonstrated the real-time stability and functional dynamics of the Nsp1-CypA/FKBP1A complex and investigated the repurposing of potential inhibitors that could block these interactions. Overall, we provided insights into the inhibitory role Nsp1 in downstream interferon production, a key aspect for host defense that prevents the SARS-CoV-2 or related family of corona virus infection

NrdR overexpression influences changes in bacterial morphology.

<p><b>(A)</b> Colony morphology of WT, ΔNrdR and OE-NrdR <i>E</i>. <i>coli</i> strains grown on LB medium. <b>(B)</b> Magnification (×100) of <i>E</i>. <i>coli</i> strains. Overexpression of NrdR resulted in bacterial aggregates (red arrows) and coccobacilli (short rods; green arrows). <b>(C)</b> Transmission electron microscopy of the WT, ΔNrdR and OE-NrdR <i>E</i>. <i>coli</i> strains at high magnification (magnification, ×21,000). Differences in flagella and cell walls among the <i>E</i>. <i>coli</i> strains can be observed.</p

Bacterial NrdR regulates adhesion to mammalian epithelial cells.

<p><b>(A)</b> Human epithelial cells in culture were infected with WT, ΔNrdR and OE-NrdR <i>E</i>. <i>coli</i> strains. Adherent bacteria were counted 3 hours after infection. Results are reported as CFUs/ml. <b>(B)</b> Direct observation of GFP-tagged WT, ΔNrdR and OE-NrdR <i>E</i>. <i>coli</i> adhering to mammalian cells by fluorescent microscopy at ×1000 magnification. The GFP signals were observed under the FITC filter of a UV laser at 475nm.</p

Complementary expression of PolA, ThiL & Eno shows partial rescue of the bacterial fitness defect caused by NrdR overexpression.

<p>The downregulated essential genes of Appa, ThiL, PolA, Eno, FbaA and Pgk were complementarily expressed under the NrdR overexpression background to test fitness rescue. Partial rescue of bacterial fitness was observed for PolA, Thil or Eno complementary expression. Complementary expression of genes Appa, FbaA and Pgk resulted in fitness defects resembling those of NrdR overexpression alone and did not result in fitness rescue. Empty vectors pET-duet (Kan⁺) and pCA24N (Cam⁺) were transformed into WT strains as controls. The <i>E</i>. <i>coli</i> with DnaK overexpression was used as both negative and positive controls by excluding or incorporating NrdR overexpression, respectively. Dilution factors for the <i>E</i>. <i>coli</i> cultures are labeled over the panels.</p

NrdR Transcription Regulation: Global Proteome Analysis and Its Role in <i>Escherichia coli</i> Viability and Virulence

<div><p>Bacterial ribonucleotide reductases (RNRs) play an important role in the synthesis of dNTPs and their expression is regulated by the transcription factors, NrdR and Fur. Recent transcriptomic studies using deletion mutants have indicated a role for NrdR in bacterial chemotaxis and in the maintenance of topoisomerase levels. However, NrdR deletion alone has no effect on bacterial growth or virulence in infected flies or in human blood cells. Furthermore, transcriptomic studies are limited to the deletion strain alone, and so are inadequate for drawing biological implications when the NrdR repressor is active or abundant. Therefore, further examination is warranted of changes in the cellular proteome in response to both NrdR overexpression, as well as deletion, to better understand its functional relevance as a bacterial transcription repressor. Here, we profile bacterial fate under conditions of overexpression and deletion of NrdR in <i>E</i>. <i>coli</i>. Biochemical assays show auxiliary zinc enhances the DNA binding activity of NrdR. We also demonstrate at the physiological level that increased <i>nrdR</i> expression causes a significant reduction in bacterial growth and fitness even at normal temperatures, and causes lethality at elevated temperatures. Corroborating these direct effects, global proteome analysis following NrdR overexpression showed a significant decrease in global protein expression. In parallel, studies on complementary expression of downregulated essential genes <i>polA</i>, <i>eno</i> and <i>thiL</i> showed partial rescue of the fitness defect caused by NrdR overexpression. Deletion of downregulated non-essential genes <i>ygfK</i> and <i>trxA</i> upon NrdR overexpression resulted in diminished bacterial growth and fitness suggesting an additional role for NrdR in regulating other genes. Moreover, in comparison with NrdR deletion, <i>E</i>. <i>coli</i> cells overexpressing NrdR showed significantly diminished adherence to human epithelial cells, reflecting decreased bacterial virulence. These results suggest that elevated expression of NrdR could be a suitable means to retard bacterial growth and virulence, as its elevated expression reduces bacterial fitness and impairs host cell adhesion.</p></div

Heat maps representing differential regulation of proteins in <i>E</i>. <i>coli</i> following NrdR-deletion and -overexpression.

<p><b>(A)</b> Protein categories upregulated in the ΔNrdR strain but downregulated in the OE-NrdR strain. <b>(B)</b> Protein categories upregulated in the ΔNrdR strain but with no change for the OE-NrdR strain. The color scale indicates differential regulation of protein amounts relative to WT <i>E</i>. <i>coli</i> control, with upregulation indicated by green shading and downregulation by red. Genes are listed alphabetically.</p

Proteomic response of <i>E</i>. <i>coli</i> to NrdR-deletion and -overexpression.

<p><b>(A)</b> LC-MS/MS resulted in identification of 818 soluble proteins of sufficient abundance to evaluate across strains. TheΔNrdR strain had more upregulated proteins compared to the wild-type, while the OE-NrdR strain had a larger percentage of downregulated proteins. The number of proteins in each category is indicated. <b>(B)</b> Selective distribution of upregulated and downregulated proteins according to log₂-fold change in the ΔNrdR (left panel) and OE-NrdR (right panel) mutants. X-axis represents the number of genes and Y-axis represents ranges of n-fold changes in protein expression.</p