Identification of intramolecular conserved G-quadruplex motifs in the genome of the bovine foamy virus-Reference-Cited by-同舟云学术

Identification of intramolecular conserved G-quadruplex motifs in the genome of the bovine foamy virus

Published:2024-06-27 Issue:2 Volume:10 Page:13-19
ISSN:2411-0388
Container-title:Journal for Veterinary Medicine, Biotechnology and Biosafety
language:en
Short-container-title:J. Vet. Med. Biotechnol. Biosafety

Author:

Balak O. K.¹,Balak S. O.²,Lymanska O. Yu.³^ORCID

Affiliation:

1. Kharkiv National Medical University, Kharkiv, Ukraine

2. Institute for Problems of Cryobiology and Cryomedicine of the National Academy of Sciences of Ukraine, Kharkiv, Ukraine

3. National Scientific Center ‘Institute of Experimental and Clinical Veterinary Medicine’, Kharkiv, Ukraine

Abstract

G-quadruplexes (G4s) are guanine-rich DNA structures, which play an essential regulatory role in key steps of the viral life cycle (replication, transcription regulation, translation). Currently, there is no relevant information about putative G4s in the bovine foamy virus (BFV) genome. The goal of the present study was the determination of such conservative non-B-DNA structures as conservative G-quadruplexes, which can be formed by two and three G-quartets in the mRNA, sense, and antisense strands of the bovine foamy virus proviral DNA. Bioinformatic analysis was used to search motifs of intramolecular G-quadruplexes in BFV mRNA and proviral DNA and to determine the G-score (a parameter that characterizes the stability of the G-quadruplex in relative units). Based on multiple alignments of 27 BFV isolates 26 putative conservative G-quadruplexes from two G-quartets were found in mRNA and sense strand of BFV proviral DNA with G-score from 30 to 36. 32 G4s formed by two G-quartets with a G-score from 30 to 36 and 2 G4s formed by three G-quartets were found in the antisense strand of BFV proviral DNA with a G-score of 53. These two G4s are direct repeats and are localized in U5 5'LTR and U5 3'-LTR. The density of G4s was 2.1/kbp in the sense strand of BFV proviral DNA and 2.8/kbp in the antisense strand. A localization map of potential stable conserved intramolecular G-quadruplexes formed by two and three G-tetrads on the BFV genome was created. Conservative G4s are unevenly distributed throughout the BFV genome. A distinctive feature of the BFV genomic organization is the fact that the antisense strand of the BFV proviral DNA is characterized by a significantly higher density of G-quadruplexes compared to one of the sense strands. The QGRS Mapper software detects a significantly higher number of potential G4s (34 G4s in the antisense strand of BFV proviral DNA) compared to the G4Hunter software (7 G4s)

Publisher

Kharkiv Entomological Society

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