Dinucleotide biases in RNA viruses that infect vertebrates or invertebrates

Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures

Dinucleotide biases have been widely investigated in the genomes of eukaryotes and viruses, but not in bacteria. We assembled a dataset of bacterial genomes (>15 000), which are representative of the genetic diversity in the kingdom Eubacteria, and we analyzed dinucleotide biases in relation to different traits. We found that TpA dinucleotides are the most depleted and that CpG dinucleotides show the widest dispersion. The abundances of both dinucleotides vary with genomic G + C content and show a very strong phylogenetic signal. After accounting for G + C content and phylogenetic inertia, we analyzed different bacterial lifestyle traits. We found that temperature preferences associate with the abundance of CpG dinucleotides, with thermophiles/hyperthemophiles being particularly depleted. Conversely, the TpA dinucleotide displays a bias that only depends on genomic G + C composition. Using predictions of intrinsic cyclizability we also show that CpG depletion may associate with higher DNA bendability in both thermophiles/hyperthermophiles and mesophiles, and that the former are predicted to have significantly more flexible genomes than the latter. We suggest that higher bendability is advantageous at high temperatures because it facilitates DNA positive supercoiling and that, through modulation of DNA mechanical properties, local or global CpG depletion controls genome organization, most likely not only in bacteria.

Syn-CpG-Spacer: A Panel web app for synonymous recoding of viral genomes with CpG dinucleotides

Vertebrate genomes contain lower than expected frequencies of the CpG dinucleotide. Consequently, many vertebrate viruses have evolved to mimic this composition, possibly in order to evade host antiviral defences (Greenbaum et al., 2008). For example, the antiviral protein ZAP binds CpGs in viral single stranded RNA with specific spacing requirements (Gonçalves-Carneiro et al., 2022), though CpGs are also likely depleted in viral genomes due to other selective pressures (Forni et al., 2023). Increasing CpG abundance by synonymous recoding could facilitate attenuation of viruses without compromising their epitope antigenicity by changing non-CpG codons to alternatives containing CpG without changing the overall amino acid sequence (Gonçalves-Carneiro et al., 2022; Le Nouën et al., 2019; Sharp et al., 2023). There are three ways CpGs can be synonymously introduced in codons: at positions 1-2 for arginine (e.g. AGA → CGA), 2-3 for several amino acids (e.g. ACA → ACG), or in a 3-1 split configuration, if a subsequent codon begins with a G (e.g. ATA-GCA → ATC-GCA). Syn-CpG-Spacer is a Python progressive web app (PWA) (MDN Web Docs, 2023) made with the Panel library (Panel Development Team, 2024) that allows for consistent recoding of viral sequences and applying biologically relevant constraints. These include setting a minimum gap between CpG's, optimising for an average CpG gap, protecting cis-acting regulatory signals from modification, and modulating the A-content in the overall sequence. The app features a sequence viewer made with the Bokeh library (Bokeh Development Team, 2024) that highlights CpG dinucleotides, allowing for efficient analysis of the resulting distribution of CpGs. This is complemented by a statistical data table. Utilising Biopython (Cock et al., 2009) modules, the user can load their sequence as a FASTA file and download the outputs as an alignment in the same format. As a PWA running on Pyodide (The Pyodide development team, 2023), the code is only executed in the user's browser and they can install the app onto their machine for offline use.

Antiviral Activity of Zinc Finger Antiviral Protein (ZAP) in Different Virus Families

The CCCH-type zinc finger antiviral protein (ZAP) in humans, specifically isoforms ZAP-L and ZAP-S, is a crucial component of the cell's intrinsic immune response. ZAP acts as a post-transcriptional RNA restriction factor, exhibiting its activity during infections caused by retroviruses and alphaviruses. Its function involves binding to CpG (cytosine-phosphate-guanine) dinucleotide sequences present in viral RNA, thereby directing it towards degradation. Since vertebrate cells have a suppressed frequency of CpG dinucleotides, ZAP is capable of distinguishing foreign genetic elements. The expression of ZAP leads to the reduction of viral replication and impedes the assembly of new virus particles. However, the specific mechanisms underlying these effects have yet to be fully understood. Several questions regarding ZAP's mechanism of action remain unanswered, including the impact of CpG dinucleotide quantity on ZAP's activity, whether this sequence is solely required for the binding between ZAP and viral RNA, and whether the recruitment of cofactors is dependent on cell type, among others. This review aims to integrate the findings from studies that elucidate ZAP's antiviral role in various viral infections, discuss gaps that need to be filled through further studies, and shed light on new potential targets for therapeutic intervention.