Overlapping Regions in HIV-1 Genome Act as Potential Sites for Host-Virus Interaction

The diverse roles of peroxisomes in the interplay between viruses and mammalian cells

Peroxisomes are ubiquitous organelles found in eukaryotic cells that play a critical role in the oxidative metabolism of lipids and detoxification of reactive oxygen species (ROS). Recently, the role of peroxisomes in viral infections has been extensively studied. Although several studies have reported that peroxisomes exert antiviral activity, evidence indicates that viruses have also evolved diverse strategies to evade peroxisomal antiviral signals. In this review, we summarize the multiple roles of peroxisomes in the interplay between viruses and mammalian cells. Focus is given on the peroxisomal regulation of innate immune response, lipid metabolism, ROS production, and viral regulation of peroxisomal biosynthesis and degradation. Understanding the interactions between peroxisomes and viruses provides novel insights for the development of new antiviral strategies.

Mutations in membrane-fusion subunit of spike glycoprotein play crucial role in the recent outbreak of COVID-19

Coronavirus disease‐2019 (COVID‐19), the ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a major threat to the entire human race. It is reported that SARS‐CoV‐2 seems to have relatively low pathogenicity and higher transmissibility than previously outbroke SARS‐CoV. To explore the reason of the increased transmissibility of SARS‐CoV‐2 compared with SARS‐CoV, we have performed a comparative analysis on the structural proteins (spike, envelope, membrane, and nucleoprotein) of two viruses. Our analysis revealed that extensive substitutions of hydrophobic to polar and charged amino acids in spike glycoproteins of SARS‐CoV2 creates an intrinsically disordered region (IDR) at the beginning of membrane‐fusion subunit and intrinsically disordered residues in fusion peptide. IDR provides a potential site for proteolysis by furin and enriched disordered residues facilitate prompt fusion of the SARS‐CoV2 with host membrane by recruiting molecular recognition features. Here, we have hypothesized that mutation‐driven accumulation of intrinsically disordered residues in spike glycoproteins play dual role in enhancing viral transmissibility than previous SARS‐coronavirus. These analyses may help in epidemic surveillance and preventive measures against COVID‐19.

Spike glycoprotein of SARS‐CoV2 experiences higher synonymous and non‐synonymous substitution rates than other three structural (E, M, N) proteins.

Extensive hydrophobic to polar and charged amino acid substitutions in S proteins during evolution from SARS‐CoV generate intrinsically disordered residues in the membrane fusion subunit (S2) of S protein.

Intrinsically disordered region at the beginning of S2 offers cleavage site of furin protease and by virtue of their flexible nature, they provide sensitive site for efficient proteolysis to activate the fusion peptide.

Enrichment of intrinsically disordered residues in fusion peptide prompts rapid fusion of viral envelop with host membrane by recruiting several MoRFs.

Intrinsic disorderness in spike glycoproteins in SARS‐CoV2 play dual role in enhancing their transmissibility than previous SARS‐corona virus.

Tobamovirus 3'-Terminal Gene Overlap May be a Mechanism for within-Host Fitness Improvement

Overlapping genes (OGs) are a universal phenomenon in all kingdoms, and viruses display a high content of OGs combined with a high rate of evolution. It is believed that the mechanism of gene overlap is based on overprinting of an existing gene. OGs help virus genes compress a maximum amount of information into short sequences, conferring viral proteins with novel features and thereby increasing their within-host fitness. Analysis of tobamovirus 3′-terminal genes reveals at least two modes of OG organization and mechanisms of interaction with the host. Originally isolated from Solanaceae species, viruses (referred to as Solanaceae-infecting) such as tobacco mosaic virus do not show 3′-terminal overlap between movement protein (MP) and coat protein (CP) genes but do contain open reading frame 6 (ORF6), which overlaps with both genes. Conversely, tobamoviruses, originally isolated from Brassicaceae species (referred to as Brassicaceae-infecting) and also able to infect Solanaceae plants, have no ORF6 but are characterized by overlapping MP and CP genes. Our analysis showed that the MP/CP overlap of Brassicaceae-infecting tobamoviruses results in the following: (i) genome compression and strengthening of subgenomic promoters; (ii) CP gene early expression directly from genomic and dicistronic MP subgenomic mRNA using an internal ribosome entry site (IRES) and a stable hairpin structure in the overlapping region; (iii) loss of ORF6, which influences the symptomatology of Solanaceae-infecting tobamoviruses; and (iv) acquisition of an IRES polypurine-rich region encoding an MP nuclear localization signal. We believe that MP/CP gene overlap may constitute a mechanism for host range expansion and virus adjustment to Brassicaceae plants.