Retroviral Psi packaging element
Encyclopedia
Retroviral Psi packaging element is a cis-acting RNA
element identified in the genomes of the retrovirus
es Human immunodeficiency virus
(HIV)
and Simian immunodeficiency virus
(SIV). It is involved in regulating the essential process of packaging the retroviral RNA genome into the viral capsid
during replication.
The final virion contains a dimer of two identical unspliced
copies of the viral genome.
In HIV, the Psi element is ∼80–150 nucleotides in length, and located at the 5' end
of the genome just upstream of the gag initiation
codon
. It has a known secondary structure composed of four hairpin
s called SL1 to SL4 (SL is for Stem-loop
) which are connected by relatively short linkers. All four stem loops are important for genome packaging and each of the stem loops SL1 , SL2 ,SL3 and SL4 has been independently expressed and structurally characterised.
Stem loop 1 (SL1) (also referred to as HIV-1_DIS) consists of a conserved hairpin structure with a palindromic
loop sequence which was predicted and confirmed by mutagenesis. This palindromic loop is known as the primary dimer initiation site (DIS) as it is believed to promote dimerization of the viral genome through formation of a “kissing dimer” intermediate. The Rfam
structure shown is based on a covariation model.
It has been shown that SL1 may provide a secondary binding site
for the viral Rev protein. The Rev protein is an essential HIV regulatory protein which increases the stability and transport of the unspliced viral RNA.
Stem-loop 2 (SL2) (also referred to as HIV-1 SD) consists of a highly conserved 19 nt stem-loop which has been shown by mutatagenis to modulate the splicing efficiency of HIV-1 mRNAs.
Stem-loop 3 (SL3) consists of a highly conserved 14 nt stem-loop which was predicted and confirmed by mutagenesis
and mass spectrometric detection (MS3D). HIV-1 SL3 is sufficient by itself to induce heterologous RNA into virus-like particles but its deletion does not completely eliminate encapsidation.
Stem-loop 4 (SL4) consists of a highly conserved 14 nt stem-loop that is located just downstream of the gag start codon. The structure was confirmed by mutagenesis
and has an NMR
and mass spectrometric detection (MS3D). It also may have coding and non-coding
roles.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
element identified in the genomes of the retrovirus
Retrovirus
A retrovirus is an RNA virus that is duplicated in a host cell using the reverse transcriptase enzyme to produce DNA from its RNA genome. The DNA is then incorporated into the host's genome by an integrase enzyme. The virus thereafter replicates as part of the host cell's DNA...
es Human immunodeficiency virus
HIV
Human immunodeficiency virus is a lentivirus that causes acquired immunodeficiency syndrome , a condition in humans in which progressive failure of the immune system allows life-threatening opportunistic infections and cancers to thrive...
(HIV)
and Simian immunodeficiency virus
SIV
SIV or Siv may refer to:* Simian immunodeficiency virus, a virus found in primates and related to HIV* Siv, a character in the children's fiction book series Guardians of Ga'Hoole...
(SIV). It is involved in regulating the essential process of packaging the retroviral RNA genome into the viral capsid
Capsid
A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic...
during replication.
The final virion contains a dimer of two identical unspliced
Splicing (genetics)
In molecular biology and genetics, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation...
copies of the viral genome.
In HIV, the Psi element is ∼80–150 nucleotides in length, and located at the 5' end
Directionality (molecular biology)
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 5′-end and a 3′-end...
of the genome just upstream of the gag initiation
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
codon
Genetic code
The genetic code is the set of rules by which information encoded in genetic material is translated into proteins by living cells....
. It has a known secondary structure composed of four hairpin
Hairpin
A hair pin or hairpin is a long device used to hold a person's hair in place.Hairpins made of metal, ivory, bronze, carved wood, etc. were used in ancient Assyria and Egypt for securing decorated hairstyles. Such hairpins suggest, as graves show, that many were luxury objects among the Egyptians...
s called SL1 to SL4 (SL is for Stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
) which are connected by relatively short linkers. All four stem loops are important for genome packaging and each of the stem loops SL1 , SL2 ,SL3 and SL4 has been independently expressed and structurally characterised.
Stem loop 1 (SL1) (also referred to as HIV-1_DIS) consists of a conserved hairpin structure with a palindromic
Palindromic sequence
A palindromic sequence is a nucleic acid sequence that is the same whether read 5' to 3' on one strand or 5' to 3' on the complementary strand with which it forms a double helix....
loop sequence which was predicted and confirmed by mutagenesis. This palindromic loop is known as the primary dimer initiation site (DIS) as it is believed to promote dimerization of the viral genome through formation of a “kissing dimer” intermediate. The Rfam
Rfam
Rfam is a database containing information about non-coding RNA families and other structured RNA elements. It is an annotated, open access database hosted by the Wellcome Trust Sanger Institute in collaboration with Janelia Farm...
structure shown is based on a covariation model.
It has been shown that SL1 may provide a secondary binding site
Binding site
In biochemistry, a binding site is a region on a protein, DNA, or RNA to which specific other molecules and ions—in this context collectively called ligands—form a chemical bond...
for the viral Rev protein. The Rev protein is an essential HIV regulatory protein which increases the stability and transport of the unspliced viral RNA.
Stem-loop 2 (SL2) (also referred to as HIV-1 SD) consists of a highly conserved 19 nt stem-loop which has been shown by mutatagenis to modulate the splicing efficiency of HIV-1 mRNAs.
Stem-loop 3 (SL3) consists of a highly conserved 14 nt stem-loop which was predicted and confirmed 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...
and mass spectrometric detection (MS3D). HIV-1 SL3 is sufficient by itself to induce heterologous RNA into virus-like particles but its deletion does not completely eliminate encapsidation.
Stem-loop 4 (SL4) consists of a highly conserved 14 nt stem-loop that is located just downstream of the gag start codon. The structure was confirmed 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...
and has an NMR
NMR
NMR may refer to:Applications of Nuclear Magnetic Resonance:* Nuclear magnetic resonance* NMR spectroscopy* Solid-state nuclear magnetic resonance* Protein nuclear magnetic resonance spectroscopy* Proton NMR* Carbon-13 NMR...
and mass spectrometric detection (MS3D). It also may have coding and non-coding
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
roles.