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Identification of G-quadruplex forming sequences in three manatee papillomaviruses
- Source :
- PLOS ONE, PLoS ONE, PLoS ONE, Vol 13, Iss 4, p e0195625 (2018)
- Publication Year :
- 2018
- Publisher :
- Public Library of Science (PLoS), 2018.
-
Abstract
- The Florida manatee (Trichechus manatus latirotris) is a threatened aquatic mammal in United States coastal waters. Over the past decade, the appearance of papillomavirus-induced lesions and viral papillomatosis in manatees has been a concern for those involved in the management and rehabilitation of this species. To date, three manatee papillomaviruses (TmPVs) have been identified in Florida manatees, one forming cutaneous lesions (TmPV1) and two forming genital lesions (TmPV3 and TmPV4). We identified DNA sequences with the potential to form G-quadruplex structures (G4) across the three genomes. G4 were located on both DNA strands and across coding and non-coding regions on all TmPVs, offering multiple targets for viral control. Although G4 have been identified in several viral genomes, including human PVs, most research has focused on canonical structures comprised of three G-tetrads. In contrast, the vast majority of sequences we identified would allow the formation of non-canonical structures with only two G-tetrads. Our biophysical analysis confirmed the formation of G4 with parallel topology in three such sequences from the E2 region. Two of the structures appear comprised of multiple stacked two G-tetrad structures, perhaps serving to increase structural stability. Computational analysis demonstrated enrichment of G4 sequences on all TmPVs on the reverse strand in the E2/E4 region and on both strands in the L2 region. Several G4 sequences occurred at similar regional locations on all PVs, most notably on the reverse strand in the E2 region. In other cases, G4 were identified at similar regional locations only on PVs forming genital lesions. On all TmPVs, G4 sequences were located in the non-coding region near putative E2 binding sites. Together, these findings suggest that G4 are possible regulatory elements in TmPVs.
- Subjects :
- 0301 basic medicine
Luminescence
Molecular biology
Trichechus manatus
Oligonucleotides
lcsh:Medicine
Biochemistry
Genome
Database and Informatics Methods
chemistry.chemical_compound
lcsh:Science
Papillomaviridae
Multidisciplinary
Nucleotides
Physics
Electromagnetic Radiation
General Medicine
Nucleic acids
Physical Sciences
Florida
Aquatic mammal
General Agricultural and Biological Sciences
Sequence Analysis
Research Article
Guanine
Bioinformatics
Biophysics
Genomics
Genome, Viral
Viral Structure
Molecular Dynamics Simulation
Biology
Research and Analysis Methods
G-quadruplex
Microbiology
Fluorescence
Biophysical Phenomena
General Biochemistry, Genetics and Molecular Biology
DNA sequencing
03 medical and health sciences
Virology
Genetics
Animals
Humans
14. Life underwater
Nucleic acid structure
DNA sequence analysis
Base Sequence
lcsh:R
Papillomavirus Infections
Biology and Life Sciences
DNA structure
DNA
G-Quadruplexes
Macromolecular structure analysis
030104 developmental biology
chemistry
Evolutionary biology
DNA, Viral
lcsh:Q
Subjects
Details
- ISSN :
- 19326203
- Volume :
- 13
- Database :
- OpenAIRE
- Journal :
- PLOS ONE
- Accession number :
- edsair.doi.dedup.....6be8e0c9908ea0bfd529ace4c0aae631