Avian HBV RNA encapsidation signal epsilon

{{Short description|RNA structure}}

File:DHBV epsilon.png

File:HHBV epsilon.jpg

{{Infobox rfam

| Name = AHBV_epsilon cis-regulatory RNA element

| image = AHBV_epsilon.jpg

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| caption = Predicted secondary structure and sequence conservation of AHBV_epsilon

| Symbol = AHBV_epsilon

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| Rfam = RF01313

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| RNA_type = Cis-reg

| Tax_domain = Viruses

| GO = {{GO|0019079}}

| SO = {{SO|0005836}}

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The Avian HBV RNA encapsidation signal epsilon (AHBV epsilon{{Cite web | url=http://rfam.org/family/RF01313 | title=Rfam: Family: AHBV_epsilon (RF01313)}}) 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.{{cite journal | vauthors = Schmid B, Rösler C, Nassal M | title = A high level of mutation tolerance in the multifunctional sequence encoding the RNA encapsidation signal of an avian hepatitis B virus and slow evolution rate revealed by in vivo infection | journal = Journal of Virology | volume = 85 | issue = 18 | pages = 9300–9313 | date = September 2011 | pmid = 21752921 | pmc = 3165760 | doi = 10.1128/JVI.05005-11 }}

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.{{cite journal | vauthors = Smith GJ, Donello JE, Lück R, Steger G, Hope TJ | title = The hepatitis B virus post-transcriptional regulatory element contains two conserved RNA stem-loops which are required for function | journal = Nucleic Acids Research | volume = 26 | issue = 21 | pages = 4818–4827 | date = November 1998 | pmid = 9776740 | pmc = 147918 | doi = 10.1093/nar/26.21.4818 }}

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. {{cite journal | vauthors = Beck J, Nassal M | title = Sequence- and structure-specific determinants in the interaction between the RNA encapsidation signal and reverse transcriptase of avian hepatitis B viruses | journal = Journal of Virology | volume = 71 | issue = 7 | pages = 4971–4980 | date = July 1997 | pmid = 9188560 | pmc = 191728 | doi = 10.1128/JVI.71.7.4971-4980.1997 }}

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.{{cite journal | vauthors = Girard FC, Ottink OM, Ampt KA, Tessari M, Wijmenga SS | title = Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals | journal = Nucleic Acids Research | volume = 35 | issue = 8 | pages = 2800–2811 | year = 2007 | pmid = 17430968 | pmc = 1885660 | doi = 10.1093/nar/gkm131 }}