Most cited article - PubMed ID 34809429
A Protein-Engineered, Enhanced Yeast Display Platform for Rapid Evolution of Challenging Targets
Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non-spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein.
- Keywords
- BA.1, BA.2, COVID-19, Omicron, SARS-CoV-2, fusogenicity, growth capacity, immune resistance, pathogenicity,
- MeSH
- COVID-19 virology MeSH
- Genome, Viral * genetics MeSH
- Spike Glycoprotein, Coronavirus * genetics MeSH
- Humans MeSH
- Mutation * MeSH
- SARS-CoV-2 * genetics pathogenicity physiology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Spike Glycoprotein, Coronavirus * MeSH
- spike protein, SARS-CoV-2 MeSH Browser
Human interleukin 24 (IL-24) is a multifunctional cytokine that represents an important target for autoimmune diseases and cancer. Since the biological functions of IL-24 depend on interactions with membrane receptors, on-demand regulation of the affinity between IL-24 and its cognate partners offers exciting possibilities in basic research and may have applications in therapy. As a proof-of-concept, we developed a strategy based on recombinant soluble protein variants and genetic code expansion technology to photocontrol the binding between IL-24 and one of its receptors, IL-20R2. Screening of non-canonical ortho-nitrobenzyl-tyrosine (NBY) residues introduced at several positions in both partners was done by a combination of biophysical and cell signaling assays. We identified one position for installing NBY, tyrosine70 of IL-20R2, which results in clear impairment of heterocomplex assembly in the dark. Irradiation with 365-nm light leads to decaging and reconstitutes the native tyrosine of the receptor that can then associate with IL-24. Photocaged IL-20R2 may be useful for the spatiotemporal control of the JAK/STAT phosphorylation cascade.
In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.
- MeSH
- COVID-19 * MeSH
- Phylogeny MeSH
- Spike Glycoprotein, Coronavirus genetics MeSH
- Cricetinae MeSH
- Humans MeSH
- Recombination, Genetic MeSH
- SARS-CoV-2 genetics MeSH
- Animals MeSH
- Check Tag
- Cricetinae MeSH
- Humans MeSH
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Spike Glycoprotein, Coronavirus MeSH
- spike protein, SARS-CoV-2 MeSH Browser
In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.
- MeSH
- Biological Assay MeSH
- COVID-19 * MeSH
- Phylogeny MeSH
- Cricetinae MeSH
- Antibodies, Neutralizing MeSH
- Antibodies, Viral MeSH
- SARS-CoV-2 genetics MeSH
- Amino Acid Substitution MeSH
- Animals MeSH
- Check Tag
- Cricetinae MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Antibodies, Neutralizing MeSH
- Antibodies, Viral MeSH
Given its highly innovative character and potential socioeconomic impact, Synthetic Biology is often ranked among prominent research areas and national research priorities in developed countries. The global evolution of this field is proceeding by leaps and bounds but its development at the level of individual states varies widely. Despite their current satisfactory economic status, the majority of 13, mostly post-communist, countries that entered the European Union family in and after 2004 (EU13) have long overlooked the blossoming of Synthetic Biology. Their prioritized lines of research have been directed elsewhere or "Synthetic Biology" did not become a widely accepted term to encompass their bioengineering and biotechnology domains. The Czech Republic is not an exception. The local SynBio mycelium already exists but is mainly built bottom-up through the activities of several academic labs, iGEM teams, and spin-off companies. In this article, we tell their individual stories and summarize the prerequisites that allowed their emergence in the Czech academic and business environment. In addition, we provide the reader with a brief overview of laboratories, research hubs, and companies that perform biotechnology and bioengineering-oriented research and that may be included in a notional "shadow SynBio community" but have not yet adopted Synthetic Biology as a unifying term for their ventures. We also map the current hindrances for a broader expansion of Synthetic Biology in the Czech Republic and suggest possible steps that should lead to the maturity of this fascinating research field in our country.
- Keywords
- Biotechnology and bioengineering, Community, Czech Republic, EU13 countries, Public perception, Research landscape, Synthetic biology, iGEM,
- Publication type
- Journal Article MeSH
The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2.75 has a greater effective reproduction number and different immunogenicity profile than BA.5. We determined the sensitivity of BA.2.75 to vaccinee and convalescent sera as well as a panel of clinically available antiviral drugs and antibodies. Antiviral drugs largely retained potency, but antibody sensitivity varied depending on several key BA.2.75-specific substitutions. The BA.2.75 spike exhibited a profoundly higher affinity for its human receptor, ACE2. Additionally, the fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were greater than those of BA.2. Our multilevel investigations suggest that BA.2.75 acquired virological properties independent of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.
- Keywords
- BA.2.75, COVID-19, Omicron, SARS-CoV-2, antiviral drug resistance, immune resistance, pathogenicity, transmissibility,
- MeSH
- Antiviral Agents pharmacology therapeutic use MeSH
- COVID-19 * MeSH
- Spike Glycoprotein, Coronavirus genetics MeSH
- Humans MeSH
- Antibodies, Neutralizing MeSH
- Antibodies, Viral MeSH
- SARS-CoV-2 * genetics MeSH
- COVID-19 Serotherapy MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Antiviral Agents MeSH
- Spike Glycoprotein, Coronavirus MeSH
- Antibodies, Neutralizing MeSH
- Antibodies, Viral MeSH
- spike protein, SARS-CoV-2 MeSH Browser
