Coronavirus 3′ UTR: Difference between revisions
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[[Coronavirus]] genomes are [[Positive-sense single-stranded RNA virus|positive-sense single-stranded]] [[RNA]] molecules with an [[untranslated region]] (UTR) at the [[Directionality (molecular biology)|3' end]] which is called the [[Five prime untranslated region|3' UTR]]. The 3' UTR is responsible for important biological functions, such as viral [[Viral replication|replication]], [[Transcription (biology)|transcription]]<ref>{{Cite journal|last=Madhugiri|first=Ramakanth|last2=Fricke|first2=Markus|last3=Marz|first3=Manja|last4=Ziebuhr|first4=John|date=2014-12-19|title=RNA structure analysis of alphacoronavirus terminal genome regions|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114417/|journal=Virus Research|volume=194|pages=76–89|doi=10.1016/j.virusres.2014.10.001|issn=0168-1702|pmc=7114417|pmid=25307890}}</ref> and packaging<ref name=":0">{{Cite journal|last=Masters|first=Paul S.|date=November 2019|title=Coronavirus genomic RNA packaging|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112113/|journal=Virology|volume=537|pages=198–207|doi=10.1016/j.virol.2019.08.031|issn=0042-6822|pmc=7112113|pmid=31505321}}</ref>. The 3' UTR has a conserved RNA [[Nucleic acid secondary structure|secondary structure]] but different Coronavirus genera (Alpha-, Beta-, Gamma-, and Deltacoronaviruses) have different structural features described below. |
[[Coronavirus]] genomes are [[Positive-sense single-stranded RNA virus|positive-sense single-stranded]] [[RNA]] molecules with an [[untranslated region]] (UTR) at the [[Directionality (molecular biology)|3' end]] which is called the [[Five prime untranslated region|3' UTR]]. The 3' UTR is responsible for important biological functions, such as viral [[Viral replication|replication]], [[Transcription (biology)|transcription]]<ref>{{Cite journal|last=Madhugiri|first=Ramakanth|last2=Fricke|first2=Markus|last3=Marz|first3=Manja|last4=Ziebuhr|first4=John|date=2014-12-19|title=RNA structure analysis of alphacoronavirus terminal genome regions|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114417/|journal=Virus Research|volume=194|pages=76–89|doi=10.1016/j.virusres.2014.10.001|issn=0168-1702|pmc=7114417|pmid=25307890}}</ref> and packaging<ref name=":0">{{Cite journal|last=Masters|first=Paul S.|date=November 2019|title=Coronavirus genomic RNA packaging|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112113/|journal=Virology|volume=537|pages=198–207|doi=10.1016/j.virol.2019.08.031|issn=0042-6822|pmc=7112113|pmid=31505321}}</ref>. The 3' UTR has a conserved RNA [[Nucleic acid secondary structure|secondary structure]] but different Coronavirus genera (Alpha-, Beta-, Gamma-, and Deltacoronaviruses) have different structural features described below. |
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== Alphacoronavirus 3' UTR == |
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The 3' UTR of [[Alphacoronavirus|Alphacoronaviruses]] consists of two small hairpins ('''PK-SL2''') which can form an alternate conformation ('''PK-SL1''') where the loop region of the second hairpin interacts with the stem of the first hairpin (see [[Coronavirus 3' UTR pseudoknot]]). PK-SL2 has been confirmed in [[Human coronavirus 229E|HCoV-229E]] and [[Human coronavirus NL63|HCoV-NL63]] by in vitro structure probing experiments. Downstream of this pseudoknot lies the '''hypervariable region''' (HVR), which is supported by many covarying base pairs in alphacoronaviruses. Further, a conserved octanucleotide sequence <code>5'-GGAAGAGC-3'</code> is present in the HVR. |
The 3' UTR of [[Alphacoronavirus|Alphacoronaviruses]] consists of two small hairpins ('''PK-SL2''') which can form an alternate conformation ('''PK-SL1''') where the loop region of the second hairpin interacts with the stem of the first hairpin (see [[Coronavirus 3' UTR pseudoknot]]). PK-SL2 has been confirmed in [[Human coronavirus 229E|HCoV-229E]] and [[Human coronavirus NL63|HCoV-NL63]] by in vitro structure probing experiments. Downstream of this pseudoknot lies the '''hypervariable region''' (HVR), which is supported by many covarying base pairs in alphacoronaviruses. Further, a conserved octanucleotide sequence <code>5'-GGAAGAGC-3'</code> is present in the HVR. |
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== Betacoronavirus 3' UTR == |
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The 3' UTR of [[Betacoronavirus|Betacoronaviruses]] is approximately 300-500 nucleotides long. The most 5' structure is the '''bulged stem-loop''' (BSL), starting downstream of the N gene [[stop codon]] and is essential for viral replication. It is predicted to be conserved among Betacoronaviruses. Downstream to the BSL lies the '''hypervariable bulged-stemloop region''' (HVR), containing a triple helix junction. The hairpin stem-loop arising from this junction participates in the pseudoknot pairing with the BSL region. The pseudoknot and the BSL partially overlap and therefore cannot be formed at the same time. It is proposed that the BSL and pseudoknot act as a molecular switch that may regulate a transition during viral RNA synthesis. Part of the HVR is the octanucleotide sequence <code>5'-GGAAGAGC-3'</code> which is conserved among Alpha- and Betacoronaviruses. The 3' UTR of [[SARS-CoV-2]] is similar to other Betacoronaviruses and is approximately 300-500 nucleotides long. |
The 3' UTR of [[Betacoronavirus|Betacoronaviruses]] is approximately 300-500 nucleotides long. The most 5' structure is the '''bulged stem-loop''' (BSL), starting downstream of the N gene [[stop codon]] and is essential for viral replication. It is predicted to be conserved among Betacoronaviruses. Downstream to the BSL lies the '''hypervariable bulged-stemloop region''' (HVR), containing a triple helix junction. The hairpin stem-loop arising from this junction participates in the pseudoknot pairing with the BSL region. The pseudoknot and the BSL partially overlap and therefore cannot be formed at the same time. It is proposed that the BSL and pseudoknot act as a molecular switch that may regulate a transition during viral RNA synthesis. Part of the HVR is the octanucleotide sequence <code>5'-GGAAGAGC-3'</code> which is conserved among Alpha- and Betacoronaviruses. The 3' UTR of [[SARS-CoV-2]] is similar to other Betacoronaviruses and is approximately 300-500 nucleotides long. |
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== Gammacoronavirus 3' UTR == |
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In [[Gammacoronavirus|Gammacoronaviruses]] a stem-loop located at the 3' UTR is observed, which is vital for viral replication. Even though a nearby pseudoknot structure, which has been observed in other genera of coronaviruses, is present, its functional importance has not been established yet. |
In [[Gammacoronavirus|Gammacoronaviruses]] a stem-loop located at the 3' UTR is observed, which is vital for viral replication. Even though a nearby pseudoknot structure, which has been observed in other genera of coronaviruses, is present, its functional importance has not been established yet. |
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== Deltacoronavirus 3' UTR == |
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There are two smaller hairpins and the hypervariable region (HVR) present in the 3' UTR of [[Deltacoronavirus|Deltacoronaviruses]]. The pseudoknot structure which is typical for Alpha- and Betacoronaviruses has not been predicted in Deltacoronaviruses so far. |
There are two smaller hairpins and the hypervariable region (HVR) present in the 3' UTR of [[Deltacoronavirus|Deltacoronaviruses]]. The pseudoknot structure which is typical for Alpha- and Betacoronaviruses has not been predicted in Deltacoronaviruses so far. |
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Revision as of 17:48, 17 April 2020
Coronavirus genomes are positive-sense single-stranded RNA molecules with an untranslated region (UTR) at the 3' end which is called the 3' UTR. The 3' UTR is responsible for important biological functions, such as viral replication, transcription[1] and packaging[2]. The 3' UTR has a conserved RNA secondary structure but different Coronavirus genera (Alpha-, Beta-, Gamma-, and Deltacoronaviruses) have different structural features described below.
Alphacoronavirus 3' UTR
The 3' UTR of Alphacoronaviruses consists of two small hairpins (PK-SL2) which can form an alternate conformation (PK-SL1) where the loop region of the second hairpin interacts with the stem of the first hairpin (see Coronavirus 3' UTR pseudoknot). PK-SL2 has been confirmed in HCoV-229E and HCoV-NL63 by in vitro structure probing experiments. Downstream of this pseudoknot lies the hypervariable region (HVR), which is supported by many covarying base pairs in alphacoronaviruses. Further, a conserved octanucleotide sequence 5'-GGAAGAGC-3' is present in the HVR.
Betacoronavirus 3' UTR
The 3' UTR of Betacoronaviruses is approximately 300-500 nucleotides long. The most 5' structure is the bulged stem-loop (BSL), starting downstream of the N gene stop codon and is essential for viral replication. It is predicted to be conserved among Betacoronaviruses. Downstream to the BSL lies the hypervariable bulged-stemloop region (HVR), containing a triple helix junction. The hairpin stem-loop arising from this junction participates in the pseudoknot pairing with the BSL region. The pseudoknot and the BSL partially overlap and therefore cannot be formed at the same time. It is proposed that the BSL and pseudoknot act as a molecular switch that may regulate a transition during viral RNA synthesis. Part of the HVR is the octanucleotide sequence 5'-GGAAGAGC-3' which is conserved among Alpha- and Betacoronaviruses. The 3' UTR of SARS-CoV-2 is similar to other Betacoronaviruses and is approximately 300-500 nucleotides long.
Gammacoronavirus 3' UTR
In Gammacoronaviruses a stem-loop located at the 3' UTR is observed, which is vital for viral replication. Even though a nearby pseudoknot structure, which has been observed in other genera of coronaviruses, is present, its functional importance has not been established yet.
Deltacoronavirus 3' UTR
There are two smaller hairpins and the hypervariable region (HVR) present in the 3' UTR of Deltacoronaviruses. The pseudoknot structure which is typical for Alpha- and Betacoronaviruses has not been predicted in Deltacoronaviruses so far.
See also
- Coronavirus 5' UTR
- Coronavirus 3' UTR pseudoknot
- Coronavirus 3' stem-loop II-like motif (s2m)
- Coronavirus frameshifting stimulation element
- Coronavirus packaging signal
- ^ Madhugiri, Ramakanth; Fricke, Markus; Marz, Manja; Ziebuhr, John (2014-12-19). "RNA structure analysis of alphacoronavirus terminal genome regions". Virus Research. 194: 76–89. doi:10.1016/j.virusres.2014.10.001. ISSN 0168-1702. PMC 7114417. PMID 25307890.
- ^ Masters, Paul S. (November 2019). "Coronavirus genomic RNA packaging". Virology. 537: 198–207. doi:10.1016/j.virol.2019.08.031. ISSN 0042-6822. PMC 7112113. PMID 31505321.