Phylogenetic Analysis and Structural Predictions of Human Adenovirus Penton Proteins as a Basis for Tissue-Specific Adenovirus Vector Design

Abstract

The penton base is a major capsid protein of human adenoviruses (HAdV) which forms the vertices of the capsid and interacts with hexon and fiber protein. Two hypervariable loops of the penton are exposed on the capsid surface. Sequences of these and 300 adjacent amino acid residues of all 51 HAdV and closely related simian adenoviruses were studied. Adjacent sequences and predicted overall secondary structure were conserved. Phylogenetic analysis revealed clustering corresponding to the HAdV species and recombination events in the origin of HAdV prototypes. All HAdV except serotypes 40 and 41 of species F exhibited an integrin binding RGD motif in the second loop. The lengths of the loops (HVR1 and RGD loops) varied significantly between HAdV species with the longest RGD loop observed in species C and the longest HVR1 in species B. Long loops may permit the insertion of motifs that modify tissue tropism. Genetic analysis of HAdV prime strain p17H30, a neutralization variant of HAdV-D17, indicated the significance of nonhexon neutralization epitopes for HAdV immune escape. Fourteen highly conserved motifs of the penton base were analyzed by site-directed mutagenesis of HAdV-D8 and tested for sustained induction of early cytopathic effects. Thus, three new motifs essential for penton base function were identified additionally to the RGD site, which interacts with a secondary cellular receptor responsible for internalization. Therefore, our penton primary structure data and secondary structure modeling in combination with the recently published fiber knob sequences may permit the rational design of tissue-specific adenoviral vectors.

Phylogeny and primary structure analysis of fiber shafts of all human adenovirus types for rational design of adenoviral gene-therapy vectors

“…Sequences of adenovirus fiber shaft clustered according to the species concept, as observed previously for the hexon e determinant, the penton base d determinant and the c determinant of the fiber knob (Madisch et al, 2005(Madisch et al, , 2007. Clustering was supported by high bootstrap values.…”

“…Clustering was supported by high bootstrap values. Interspecies variability in the shaft region was higher (55-93 % amino acid sequence divergence) than in the fiber knob region (50-59 %) (Madisch et al, 2007); in contrast, intraspecies divergence was higher in the knob region (18-53 % amino acid sequence divergence) than in the fiber shaft (18-44 %). Surprisingly, all HAdV species except for HAdV-B showed a lower intraspecies ratio of synonymous/nonsynonymous (S/N) mutations in the fiber shaft (e.g.…”

Diversity of adenoviruses detected in children less than 5 years of age hospitalized with lower acute respiratory infection in Paraguay, 2010-2013

“…Se emplearon cebadores ya publicados para (17) (18) amplificar los genes hexon y penton . Sin embargo, fue necesario el diseño de nuevos cebadores para el gen fibra de cada especie de HAdV, debido a la dificultad de amplificar este gen en muestras clínicas con los cebadores disponibles.…”

“…En cuanto al gen hexon, se amplificó la región C4, (17) empleando dos pares de cebadores , que amplifican de forma genérica todas las especies de HAdV sin distinción de genotipos. En cuanto al gen penton, se amplificó la región que contiene el motivo (18) RGD, utilizando tres pares de cebadores , un par para cada especie (B, C y D). En cuanto al gen fibra, se amplificó un fragmento que incluía las regiones shaft/knob (en cuyos límites se han reportado eventos de recombinación); se diseñaron los cebadores forward para las especies B y D, y se emparejaron con (9) cebadores descritos previamente .…”

Human Adenovirus Type 52: a Type 41 in Disguise?

“…4, HAdV-52 is clearly separated from HAdV-40 and -41. Three significant characteristics of the HAdV-52 genome include the presence of an integrin-binding site (RGD motif) on the penton base and the presence of genes for the 12.5-kilodalton E3 protein and the dUTPase, all of which are absent in HAdV-40 and -41 (4,6).…”