Avian HBV RNA encapsidation signal epsilon

The Avian HBV RNA encapsidation signal epsilon (AHBV epsilon[1]) is an RNA structure that is shown to facilitate encapsidation of the pregenomic RNA required for viral replication. There are two main classes of encapsidation signals in avian hepatitis B viruses - Duck hepatitis B virus (DHBV) and Heron hepatitis B virus (HHBV) like. DHBV is used as a model to understand human Hepatitis B virus. Although studies have shown that the HHBV epsilon has less pairing in the upper stem than DHBV, this pairing is not absolutely required for DHBV infection in ducks.[2]

Fig. 1. Duck HBV RNA encapsidation signal epsilon

Fig. 2. Heron HBV RNA encapsidation signal epsilon

AHBV_epsilon cis-regulatory RNA element
Predicted secondary structure and sequence conservation of AHBV_epsilon
Identifiers
Symbol	AHBV_epsilon
Rfam	RF01313
Other data
RNA type	Cis-reg
Domain(s)	Viruses
GO	GO:0019079
SO	SO:0005836
PDB structures	PDBe

DHBV epsilon consists of a stem structure, a bulge and an apical loop (Fig. 1). The RNA structure was determined by chemical probing, NMR analysis and by mutagenesis.[3]

HHBV epsilon also consists of a stem structure, a bulge and an apical loop (Fig. 2). The RNA structure has been determined by chemical probing and by mutagenesis. However, it has less base pairing in the upper stem than DHBV epsilon. [4]

Recent NMR analysis of both the HHBV and DHBV epsilon have shown that the apical loop to be capped by a stable well-structured UGUU tetraloop.[5]

In the Rfam database a single covariation model (AHBV_epsilon box right) best discriminates between the true instances of the element in sequence databases and background. The secondary structure diagram is a computer generated view of the structure with highly conserved bases shown in red. It includes the major elements shown in Figures 1 and 2.