Genome-Wide Analysis Of The Viral G-Quadruplex And Its Investigation As Target Of Plant Virus Inhibitor

Discovering new targets and developing antiviral drugs can effectively reduce the damage of animal and plant viruses on our country's economic development and people's health.G-quadruplex,formed through guanine rich nucleic sequence,can dynamically regulate human viral gene expression,and chemical compounds targeting G-quadruplexes exhibit strong antiviral activity.There are also many putative quadruplex-forming sequences(PQS)in the plant virus genome.However,the intracellular environment of different organisms varies differently,and the feasibility of G-quadruplex as an antiviral drug target needs further exploration.In this work,the method of bioinformatics was applied to predict the PQS in all reference virus genomes.The viral putative G-quadruplex database was established.Then the evolutionary biology was applied to comprehensively analyze the distribution,conservation,and structural stability of PQSs in virus genomes with different host and genome types.The PQS sequences of plant viruses were selected from the ViPGD database,and the methods of biophysics were used to explore the feasibility of using G-quadruplexes as targets for anti-plant virus drugs.The ViPGD database allowed users to retrieve the sequence,distribution,location,conservation,structural stability,and other information about PQSs in different virus genmes through different searching methods.Furthermore,the ViPGD also surported users to carry out the personalized analysis to the PQS pattern conservation.Distribution and abundance analysis showed that the PQS in the viral genomes occurred non-randomly and the viral genome tended to form G₂-PQS instead of G₃-PQS.The analysis of codon usage bias showed that the G₂-PQS was more likely to exist in the virus coding region compared to G₃-PQS.Conservation analysis indicated that the G₂-PQS instead of G₃-PQS was conserved in the viral genomes.The structural stability analysis of G-quadruplex showed that the eukaryotic virus had the higher G-quadruplex structural stability than the prokaryotic virus,suggesting that the virus PQS was under different selective pressures from the hosts.Biophysical experiments showed that the G-quadruplex ligand NMM(N-Methylmesoporphyrin ?)had a better performance to prevent the Tobacco mosaic virus(TMV)reproduction and had a good viral inhibitory activity and therapeutic activity,suggesting that NMM may affect the replication of the TMV genome by stabilizing the RNA G₂-quadruplex structure of TMV.Overall,the viral PQS database at the whole genome level was first established in this study.And our data showed that the occurrence of PQS in the viral genome may be affected by the host cell types.The G₂-quadruplex tend to play more important roles in virus biology than the G₃-quadruplex and had a higher potential to be used as targets for antiviral drugs.This study might deepen the understanding of the viral G-quadruplex and provided a favorable basis for the screening of viral G-quadruplex drug targets.And this research provides a good research tool and example for the development of new green pesticide targets.