Heron HBV RNA encapsidation signal epsilon
Encyclopedia
The Avian HBV RNA encapsidation signal epsilon (AHBV_epsilon) is an RNA structure
that is shown to facilitate encapsidation of the pregenomic RNA required for replication
. There are two main classes of encapsidation signals in avian HBV viruses - Duck hepatitis B virus (DHBV) and Heron hepatitis B virus (HHBV) like. DHBV is used as a model to understand human HBV. 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.
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
.
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.
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.
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.
RNA structure
Biomolecular structure is the structure of biomolecules, mainly proteins and the nucleic acids DNA and RNA. The structure of these molecules is frequently decomposed into primary structure, secondary structure, tertiary structure, and quaternary structure. The scaffold for this structure is...
that is shown to facilitate encapsidation of the pregenomic RNA required for replication
Viral replication
Viral replication is the term used by virologists to describe the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. From the perspective of the virus, the purpose of viral replication is...
. There are two main classes of encapsidation signals in avian HBV viruses - Duck hepatitis B virus (DHBV) and Heron hepatitis B virus (HHBV) like. DHBV is used as a model to understand human HBV. 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.
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
NMR spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy, is a research technique that exploits the magnetic properties of certain atomic nuclei to determine physical and chemical properties of atoms or the molecules in which they are contained...
and by mutagenesis
Mutagenesis
Mutagenesis is a process by which the genetic information of an organism is changed in a stable manner, resulting in a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures...
.
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
Mutagenesis
Mutagenesis is a process by which the genetic information of an organism is changed in a stable manner, resulting in a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures...
. However, it has less base pairing in the upper stem than DHBV epsilon.
Recent NMR analysis
NMR spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy, is a research technique that exploits the magnetic properties of certain atomic nuclei to determine physical and chemical properties of atoms or the molecules in which they are contained...
of both the HHBV and DHBV epsilon have shown that the apical loop to be capped by a stable well-structured UGUU tetraloop.
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.