Matveev, E. V. | Search bioRxiv

bioRxiv2026

Hairpin Architecture and Extended Sequence Context Shape APOBEC3 Mutagenesis in Monkeypox Virus at Different Genomic Scales

The 2022 global mpox outbreak was characterized by an unusual accumulation of more than fifty APOBEC-signature substitutions in MPXV genomes. A previous study suggested that these substitutions preferentially occur within and near hairpins or cruciforms - stem-loop structures formed by inverted repeats. Here, we show that this conclusion resulted from an inappropriate statistical analysis and, using two substantially larger datasets, demonstrate that APOBEC-signature mutations are specifically enriched at TC motifs located at the 3' ends of hairpin loops, but not in other regions of hairpins/cruciforms or in their vicinity. We further identified a preference for stem-loop structures with longer stems and shorter loops, consistent with patterns previously reported for the APOBEC mutagenesis in cancer genomes. Our analysis also revealed a positive association between APOBEC-signature mutation propensity and hairpin stability in single-stranded DNA. Nevertheless, stem-loop structures with long stems and short loops are relatively rare in the MPXV genome, limiting their contribution to the genome-wide distribution of APOBEC-signature mutations to a predominantly local effect. In contrast, extended nucleotide context downstream of the TC motif showed strong genome-wide predictive value, with a marked preference for guanine-rich trinucleotide immediately downstream. Analysis of the upstream nucleotide context was consistent with the mutational specificity of APOBEC3A. Together, these results identify distinct structural and sequence determinants of the APOBEC-associated mutagenesis in MPXV and show that local hairpin/cruciform architecture and extended nucleotide context contribute at different genomic scales.

microbiology↗

bioRxiv2023

Genome-wide Bioinformatics Analysis of Human Protease Specificity Identified Potential Cathepsin L Cleavage Site at K790 Position of the SARS-CoV-2 Spike Glycoprotein

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) primarily enters the cell by binding the viruss spike (S) glycoprotein to the angiotensin-converting enzyme 2 (ACE2) receptor on the cell surface, followed by proteolytic cleavage by host proteases. Studies have identified furin and TMPRSS2 proteases in priming and triggering cleavages of the S glycoprotein, converting it into a fusion-competent form and initiating membrane fusion, respectively. Alternatively, SARS-CoV-2 can enter the cell through the endocytic pathway, where activation is triggered by lysosomal cathepsin L. However, other proteases are also suspected to be involved in both entry routes. In this study, we conducted a genome-wide bioinformatics analysis to explore the capacity of human proteases in hydrolyzing peptide bonds of the S glycoprotein. Predictive models of sequence specificity for 169 human proteases were constructed and applied to the S glycoprotein together with the method for predicting structural susceptibility to proteolysis of protein regions. After validating our approach on extensively studied S2 and S1/S2 cleavage sites, we applied our method to each peptide bond of the S glycoprotein across all 169 proteases. Our results indicate that various members of the PCSK, TTSP, and kallikrein families, as well as specific coagulation factors, are capable of cleaving S2 or S1/S2 sites. We have also identified a potential cleavage site of cathepsin L at the K790 position within the S2 loop. Structural analysis suggests that cleavage of this site induces conformational changes similar to the cleavage at the R815 (S2) position, leading to the exposure of the fusion peptide and subsequent fusion with the membrane. Other potential cleavage sites and the influence of mutations in common SARS-CoV-2 variants on proteolytic efficiency are discussed.

genomics↗