Sequencing and characterization of the full-length gene encoding the single-stranded DNA binding protein of a novel Chelonian herpesvirus. 2004

O Nigro, and G Yu, and A Alonso Aguirre, and Y Lu
Retrovirology Research Laboratory, Pacific Biomedical Research Center, University of Hawaii Manoa, Hawaii, USA.

Through 4 consecutive genomic walks employing a recently modified inverse polymerase chain reaction technique, a 4,054-bp DNA fragment of a newfound green turtle herpesvirus (GTHV) was obtained from tumor tissues of a green turtle with fibropapillomas. This newly identified viral DNA fragment contains two non-overlapping open reading frames (ORF) oriented in the 3' to 5' direction. The first ORF is 59% G+C rich and contains the full-length genomic sequence of the DNA binding protein (DBP) gene (3,585 bp) encoding a protein of 1,195 amino acid residues in length. The second ORF encodes a partial peptide of the UL28 gene. Phylogenetic analysis of the GTHV DBP gene confirmed and substantiated that this novel Chelonian herpesvirus is closely related to the subfamily Alphaherpesvirinae. Examination of the translated amino acid sequence further supports this categorization since GTHV DBP comprises a highly conserved zinc finger motif (CXLCX4RX2C) and a putative DNA binding domain, and exhibits high sequence homology to other alphaherpesviruses. Cloning and sequencing the genome of this putative herpesvirus will facilitate current understanding of its role in causing GTFP and the development of molecular- and immuno-based methods for the diagnosis and prevention of this devastating disease of green turtles.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D004268 DNA-Binding Proteins Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases. DNA Helix Destabilizing Proteins,DNA-Binding Protein,Single-Stranded DNA Binding Proteins,DNA Binding Protein,DNA Single-Stranded Binding Protein,SS DNA BP,Single-Stranded DNA-Binding Protein,Binding Protein, DNA,DNA Binding Proteins,DNA Single Stranded Binding Protein,DNA-Binding Protein, Single-Stranded,Protein, DNA-Binding,Single Stranded DNA Binding Protein,Single Stranded DNA Binding Proteins
D004277 DNA, Single-Stranded A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle. Single-Stranded DNA,DNA, Single Stranded,Single Stranded DNA
D005814 Genes, Viral The functional hereditary units of VIRUSES. Viral Genes,Gene, Viral,Viral Gene
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D014426 Turtles Any reptile including tortoises, fresh water, and marine species of the order Testudines with a body encased in a bony or cartilaginous shell consisting of a top (carapace) and a bottom (plastron) derived from the ribs. Sea Turtles,Terrapins,Tortoises,Sea Turtle,Terrapin,Tortoise,Turtle,Turtle, Sea,Turtles, Sea
D016335 Zinc Fingers Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites. Zinc Finger DNA-Binding Domains,Zinc Finger Motifs,Finger, Zinc,Fingers, Zinc,Motif, Zinc Finger,Motifs, Zinc Finger,Zinc Finger,Zinc Finger DNA Binding Domains,Zinc Finger Motif

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