Intensive Distribution of G2-Quaduplexes in the Pseudorabies Virus Genome and Their Sensitivity to Cations and G-Quadruplex Ligands

Abstract

Guanine-rich sequences in the genomes of herpesviruses can fold into G-quadruplexes. Compared with the widely-studied G3-quadruplexes, the dynamic G2-quadruplexes are more sensitive to the cell microenvironment, but they attract less attention. Pseudorabies virus (PRV) is the model species for the study of the latency and reactivation of herpesvirus in the nervous system. A total of 1722 G2-PQSs and 205 G3-PQSs without overlap were identified in the PRV genome. Twelve G2-PQSs from the CDS region exhibited high conservation in the genomes of the Varicellovirus genus. Eleven G2-PQSs were 100% conserved in the repeated region of the annotated PRV genomes. There were 212 non-redundant G2-PQSs in the 3′ UTR and 19 non-redundant G2-PQSs in the 5′ UTR, which would mediate gene expression in the post-transcription and translation processes. The majority of examined G2-PQSs formed parallel structures and exhibited different sensitivities to cations and small molecules in vitro. Two G2-PQSs, respectively, from 3′ UTR of UL5 (encoding helicase motif) and UL9 (encoding sequence-specific ori-binding protein) exhibited diverse regulatory activities with/without specific ligands in vivo. The G-quadruplex ligand, NMM, exhibited a potential for reducing the virulence of the PRV Ea strain. The systematic analysis of the distribution of G2-PQSs in the PRV genomes could guide further studies of the G-quadruplexes’ functions in the life cycle of herpesviruses.

Identification and characterization of two conserved G-quadruplex forming motifs in the Nipah virus genome and their interaction with G-quadruplex specific ligands

“…The nucleotide sequence comprising of at least two or more consecutive guanine residues separated by a spacer region forms G-quadruplex structures. However, only two G-tetrads are enough to form the G-quadruplex structures as depicted in viruses such as Florida manatee species infecting papillomavirus and Pseudorabies virus 32,33 . Following this notion, we performed the genome-wide screening of potential G-quadruplex forming sequences in all available isolates of NiV (Table S1) by using our previously published G-quadruplex prediction tool 34 (Table S2).…”

“…The sequences typically consist of two-guanine repeats which are capable of forming the two G-tetrad structures. These two G-tetrad G-quadruplexes have been shown to have a potential role in the viral life cycle 32,33 . The computational analysis of putative HGQs is ascertained by the biophysical assays.…”

N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA

“…Effect of NMM on infectious agents. NMM has been identified as a potential drug against the malaria parasite [75], the pseudorabies virus [71], and antigenic variation in the gonorrhea bacterium [76]. These effects are directly linked to NMM's ability to induce and stabilize GQ structures, thereby indicating that GQs are viable targets in infectious diseases.…”

Unlocking G-Quadruplexes as Antiviral Targets

“…G-Quadruplexes and Pathogens. Guanine-rich nucleic acid sequences can form a variety of structures, such as the well-known tetrahelical G-quadruplex (G4) motif, the G-triplex, G-rich hairpins, and other motifs (Deng et al, 2019). G-quadruplexes are noncanonical but ubiquitous nucleic acid structures that can be formed by G-rich DNA and RNA sequences.…”