Coronavirus 3' stem-loop II-like motif (s2m)
Encyclopedia
The Coronavirus 3' stem-loop II-like motif (also known as s2m) is a secondary structure
motif identified in the 3'untranslated region (3'UTR) of astrovirus
, coronavirus
and equine rhinovirus
genome
s. Its function is unknown, but various viral 3' UTR regions have been found to play roles in viral replication
and packaging.
This motif appears to be conserved in both nucleotide
sequence and secondary structure
folding indicating a strong evolutionary selection for its conservation
. The presence of this conserved motif in these three different viral families is suggested to be the result of at least two separate recombination
events.
Other RNA families identified in the coronavirus include the SL-III cis-acting replication element (CRE)
, the coronavirus frameshifting stimulation element
, the coronavirus packaging signal
and the coronavirus 3' UTR pseudoknot
.
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
motif identified in the 3'untranslated region (3'UTR) of astrovirus
Astrovirus
Astrovirus is a type of virus that was first discovered in 1975 using electron microscopes following an outbreak of diarrhoea in humans. In addition to humans, astroviruses have now been isolated from numerous mammalian animal species and from avian species such as ducks, chickens, and turkey...
, coronavirus
Coronavirus
Coronaviruses are species in the genera of virus belonging to the subfamily Coronavirinae in the family Coronaviridae. Coronaviruses are enveloped viruses with a positive-sense single-stranded RNA genome and a helical symmetry. The genomic size of coronaviruses ranges from approximately 16 to 31...
and equine rhinovirus
Rhinovirus
Human rhinoviruses are the most common viral infective agents in humans and are the predominant cause of the common cold. Rhinovirus infection proliferates in temperatures between 33–35 °C , and this may be why it occurs primarily in the nose...
genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s. Its function is unknown, but various viral 3' UTR regions have been found to play roles in viral 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...
and packaging.
This motif appears to be conserved in both nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
sequence and secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
folding indicating a strong evolutionary selection for its conservation
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...
. The presence of this conserved motif in these three different viral families is suggested to be the result of at least two separate recombination
Recombination
Recombination may refer to:* Recombination , the process by which genetic material is broken and joined to other genetic material* Recombination , in semiconductors, the elimination of mobile charge carriers...
events.
Other RNA families identified in the coronavirus include the SL-III cis-acting replication element (CRE)
Coronavirus SL-III cis-acting replication element (CRE)
The coronavirus SL-III cis-acting replication element is an RNA element that regulates defective interfering RNA replication.Other RNA families identified in the coronavirus include the coronavirus 3' stem-loop II-like motif , the coronavirus frameshifting stimulation element, the coronavirus...
, the coronavirus frameshifting stimulation element
Coronavirus frameshifting stimulation element
In molecular biology, the coronavirus frameshifting stimulation element is a conserved stem-loop of RNA found in coronaviruses that can promote ribosomal frameshifting. Such RNA molecules interact with a downstream region to form a pseudoknot structure; the region varies according to the virus but...
, the coronavirus packaging signal
Coronavirus packaging signal
The Coronavirus packaging signal is a conserved cis-regulatory element found in Coronavirus which has an important role in regulating the packaging of the viral genome into the capsid....
and the coronavirus 3' UTR pseudoknot
Coronavirus 3' UTR pseudoknot
The Coronavirus 3' UTR pseudoknot is an RNA structure found in the coronavirus genome. Coronaviruses contain 30 kb single-stranded positive-sense RNA genomes. The 3' UTR region of these coronavirus genomes contains a conserved ~55 nucleotide pseudoknot structure which is necessary for viral genome...
.