scholarly journals The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics

2020 ◽  
Author(s):  
Xin Li ◽  
Xiufeng Jin ◽  
Shunmei Chen ◽  
Liangge Wang ◽  
Tung On Yau ◽  
...  
Keyword(s):  
Viral Entry ◽  
Binding Sites ◽  
Cleavage Sites ◽  
Specific Receptor ◽  
Furin Cleavage ◽  
Translational Initiation ◽  
Ribosome Binding Sites ◽  
Gene Level ◽  
Main Factors ◽  
First Time

AbstractIn December 2019, the world awoke to a new zoonotic strain of coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In the present study, we identified key recombination regions and mutation sites cross the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters of betacoronavirus subgroup B. Based on the analysis of these recombination events, we proposed that the Spike protein of SARS-CoV-2 may have more than one specific receptor for its function. In addition, we reported—for the first time—a recombination event of ORF8 at the whole-gene level in a bat and ultimately determined that ORF8 enhances the viral replication. In conjunction with our previous discoveries, we found that receptor binding abilities, junction furin cleavage sites (FCSs), strong first ribosome binding sites (RBSs) and enhanced ORF8s are main factors contributing to transmission, virulence and host adaptability of CoVs. Junction FCSs and enhanced ORF8s increase the efficiencies in viral entry into cells and replication, respectively while strong first RBSs enhance the translational initiation. The strong recombination ability of CoVs integrated these factors to generate multiple recombinant strains, two of which evolved into SARS-CoV and SARS-CoV-2 by nature selection, resulting in the SARS and COVID-19 pandemics.

scholarly journals Genomic Feature Analysis of Betacoronavirus Provides Insights Into SARS and COVID-19 Pandemics

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Li ◽  
Jia Chang ◽  
Shunmei Chen ◽  
Liangge Wang ◽  
Tung On Yau ◽  
...  
Keyword(s):  
Feature Analysis ◽  
Genomic Feature ◽  
Cleavage Sites ◽  
Furin Cleavage ◽  
Genomic Features ◽  
Future Studies ◽  
Origin And Evolution ◽  
The World ◽  
Main Factors ◽  
Similar Risk

In December 2019, the world awoke to a new betacoronavirus strain named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Betacoronavirus consists of A, B, C and D subgroups. Both SARS-CoV and SARS-CoV-2 belong to betacoronavirus subgroup B. In the present study, we divided betacoronavirus subgroup B into the SARS1 and SARS2 classes by six key insertions and deletions (InDels) in betacoronavirus genomes, and identified a recently detected betacoronavirus strains RmYN02 as a recombinant strain across the SARS1 and SARS2 classes, which has potential to generate a new strain with similar risk as SARS-CoV and SARS-CoV-2. By analyzing genomic features of betacoronavirus, we concluded: (1) the jumping transcription and recombination of CoVs share the same molecular mechanism, which inevitably causes CoV outbreaks; (2) recombination, receptor binding abilities, junction furin cleavage sites (FCSs), first hairpins and ORF8s are main factors contributing to extraordinary transmission, virulence and host adaptability of betacoronavirus; and (3) the strong recombination ability of CoVs integrated other main factors to generate multiple recombinant strains, two of which evolved into SARS-CoV and SARS-CoV-2, resulting in the SARS and COVID-19 pandemics. As the most important genomic features of SARS-CoV and SARS-CoV-2, an enhanced ORF8 and a novel junction FCS, respectively, are indispensable clues for future studies of their origin and evolution. The WIV1 strain without the enhanced ORF8 and the RaTG13 strain without the junction FCS “RRAR” may contribute to, but are not the immediate ancestors of SARS-CoV and SARS-CoV-2, respectively.

scholarly journals The Discovery of a Recombinant SARS2-like CoV Strain Provides Insight Into SARS and COVID-19 Pandemics

2020 ◽  
Author(s):  
Xin Li ◽  
Xiufeng Jin ◽  
Shunmei Chen ◽  
Liangge Wang ◽  
Tung On Yau ◽  
...  
Keyword(s):  
Junction Region ◽  
Entry Site ◽  
Furin Cleavage ◽  
Internal Ribosome Entry ◽  
Spike Gene ◽  
Furin Cleavage Site ◽  
Gene Level ◽  
First Time ◽  
Insight Into

Abstract Background: In December 2019, the world awoke to a new zoonotic strain of coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).Results: In the present study, we classified betacoronavirus subgroup B into the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters, and the ORF8 genes of these three clusters into types 1, 2 and 3, respectively. One important result of our study is that we reported—for the first time—a recombination event of ORF8 at the whole-gene level in a bat, which had been co-infected by two betacoronavirus strains. This result provides substantial proof for long-existing hypotheses regarding the recombination and biological functions of ORF8. Based on the analysis of recombination events in the Spike gene, we propose that the Spike protein of SARS-CoV-2 may have more than one specific receptor for its function as gp120 of HIV has CD4 and CCR5. In the present study, we also found that the ancestor of betacoronavirus had a strong first Internal Ribosome Entry Site (IRES) and at least one furin cleavage site (FCS) in the junction region between S1 and S2 subunits.Conclusions: We concluded that the junction FCS in SARS-CoV-2 may increase the efficiency of its entry into cells, while the type 2 ORF8 acquired by SARS-CoV may increase its replication efficiency. These two most critical events provide the most likely explanation for SARS and COVID-19 pandemics.

Design of Ribosome Binding Sites in Streptomyces coelicolor

2017 ◽  
Vol 14 (4) ◽  
Author(s):  
Hong-Dou Luo ◽  
Yang Tao ◽  
Wen-Guang Wang ◽  
Tao Lin ◽  
Yue-Yue Wang ◽  
...  
Keyword(s):  
Binding Sites ◽  
Streptomyces Coelicolor ◽  
Ribosome Binding ◽  
Ribosome Binding Sites

Redox Potential - (Electronic) Structure Relationships in 18- and 17-Electron Mononitrile (or Monocarbonyl) Diphosphine Complexes of Re and Fe

2001 ◽  
Vol 66 (1) ◽  
pp. 139-154 ◽  
Author(s):  
M. Fátima C. Guedes Da Silva ◽  
Luísa M. D. R. S. Martins ◽  
João J. R. Fraústo Da Silva ◽  
Armando J. L. Pombeiro
Keyword(s):  
Cyclic Voltammetry ◽  
Electronic Structure ◽  
Binding Sites ◽  
Closed Shell ◽  
Carbonyl Complexes ◽  
Metal Centre ◽  
Pt Electrode ◽  
Metal Site ◽  
Oxidation Potentials ◽  
First Time

The organonitrile or carbonyl complexes cis-[ReCl(RCN)(dppe)2] (1) (R = 4-Et2NC6H4 (1a), 4-MeOC6H4 (1b), 4-MeC6H4 (1c), C6H5 (1d), 4-FC6H4 (1e), 4-ClC6H4 (1f), 4-O2NC6H4 (1g), 4-ClC6H4CH2 (1h), t-Bu (1i); dppe = Ph2PCH2CH2PPh2), or cis-[ReCl(CO)(dppe)2] (2), as well as trans-[FeBr(RCN)(depe)2]BF4 (3) (R = 4-MeOC6H4 (3a), 4-MeC6H4 (3b), C6H5 (3c), 4-FC6H4 (3d), 4-O2NC6H4 (3e), Me (3f), Et (3g), 4-MeOC6H4CH2 (3h); depe = Et2PCH2CH2PEt2), novel trans-[FeBr(CO)(depe)2]BF4 (4) and trans-[FeBr2(depe)2] (5) undergo, as revealed by cyclic voltammetry at a Pt-electrode and in aprotic non-aqueous medium, two consecutive reversible or partly reversible one-electron oxidations assigned as ReI → ReII → ReIII or FeII → FeIII → FeIV. The corresponding values of the oxidation potentials IE1/2ox and IIE1/2ox (waves I and II, respectively) correlate with the Pickett's and Lever's electrochemical ligand and metal site parameters. This allows to estimate these parameters for the various nitrile ligands, depe and binding sites (for the first time for a FeIII/IV couple). The electrochemical ligand parameter show dependence on the "electron-richness" of the metal centre. The values of IE1/2ox for the ReI complexes provide some supporting for a curved overall relationship with the sum of Lever's electrochemical ligand parameter. The Pickett parametrization for closed-shell complexes is extended now also to 17-electron complexes, i.e. with the 15-electron ReII and FeIII centres in cis-{[ReCl(dppe)2]}+ and trans-{FeBr(depe)2}2+, respectively.

scholarly journals Tuning a bi-enzymatic cascade reaction in Escherichia coli to facilitate NADPH regeneration for ε-caprolactone production

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jinghui Xiong ◽  
Hefeng Chen ◽  
Ran Liu ◽  
Hao Yu ◽  
Min Zhuo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Binding Sites ◽  
Regeneration System ◽  
Nadph Regeneration ◽  
Whole Cell ◽  
Cyclohexanone Monooxygenase ◽  
Ribosome Binding ◽  
Ribosome Binding Sites ◽  
Whole Cell Biocatalyst ◽  
Substrate Tolerance

Abstractε-Caprolactone is a monomer of poly(ε-caprolactone) which has been widely used in tissue engineering due to its biodegradability and biocompatibility. To meet the massive demand for this monomer, an efficient whole-cell biocatalytic approach was constructed to boost the ε-caprolactone production using cyclohexanol as substrate. Combining an alcohol dehydrogenase (ADH) with a cyclohexanone monooxygenase (CHMO) in Escherichia coli, a self-sufficient NADPH-cofactor regeneration system was obtained. Furthermore, some improved variants with the better substrate tolerance and higher catalytic ability to ε-caprolactone production were designed by regulating the ribosome binding sites. The best mutant strain exhibited an ε-caprolactone yield of 0.80 mol/mol using 60 mM cyclohexanol as substrate, while the starting strain only got a conversion of 0.38 mol/mol when 20 mM cyclohexanol was supplemented. The engineered whole-cell biocatalyst was used in four sequential batches to achieve a production of 126 mM ε-caprolactone with a high molar yield of 0.78 mol/mol.

Expression of synthetic calcitonin genes in plasmid vectors containing tandemly repeated non-overlapping ribosome binding sites

1989 ◽  
Vol 21 (9) ◽  
pp. 987-996 ◽  
Author(s):  
Krassimir Alexciev ◽  
Anna Uscheva ◽  
Maja Pavlova ◽  
Libert Yavachev ◽  
Ivan Ivanov
Keyword(s):  
Binding Sites ◽  
Plasmid Vectors ◽  
Ribosome Binding ◽  
Ribosome Binding Sites

scholarly journals Furin cleavage sites naturally occur in coronaviruses

2021 ◽  
Vol 50 ◽  
pp. 102115
Author(s):  
Yiran Wu ◽  
Suwen Zhao
Keyword(s):  
Cleavage Sites ◽  
Furin Cleavage

scholarly journals Mouse IgG3 binding to macrophage-like cells is prevented by deglycosylation of the antibody or by Accutase treatment of the cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alicja Karabasz ◽  
Monika Bzowska ◽  
Joanna Bereta ◽  
Maria Czarnek ◽  
Maja Sochalska ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Complex Network ◽  
Immune Cells ◽  
Specific Receptor ◽  
Fcγ Receptors ◽  
Specific Receptors ◽  
First Time

AbstractThe binding of mouse IgG3 to Fcγ receptors (FcγR) and the existence of a mouse IgG3-specific receptor have been discussed for 40 years. Recently, integrin beta-1 (ITGB1) was proposed to be a part of an IgG3 receptor involved in the phagocytosis of IgG3-coated pathogens. We investigated the interaction of mouse IgG3 with macrophage-like J774A.1 and P388D1 cells. The existence of an IgG3-specific receptor was verified using flow cytometry and a rosetting assay, in which erythrocytes clustered around the macrophage-like cells coated with an erythrocyte-specific IgG3. Our findings confirmed that receptors binding antigen-free IgG3 are present on J774A.1 and P388D1 cells. We demonstrated for the first time that the removal of N-glycans from IgG3 completely abolished its binding to the cells. Moreover, we discovered that the cells treated with Accutase did not bind IgG3, indicating that IgG3-specific receptors are substrates of this enzyme. The results of antibody-mediated blocking of putative IgG3 receptors suggested that apart from previously proposed ITGB1, FcγRII, FcγRIII, also additional, still unknown, receptor is involved in IgG3 binding. These findings indicate that there is a complex network of glycan-dependent interactions between mouse IgG3 and the surface of effector immune cells.

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