Coronavirus Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the com ...

genomes are positive-sense single-stranded

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

molecules with an untranslated region (UTR) at the

3′ end Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide pentose-sugar-ri ...

which is called the

3′ UTR In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. The 3′-UTR often contains regulatory regions that post-transcriptionally ...

. The 3′ UTR is responsible for important biological functions, such as viral replication. The 3′ UTR has a conserved RNA

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

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 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 ...

). PK-SL2 has been confirmed in

HCoV-229E ''Human coronavirus 229E'' (''HCoV-229E'') is a species of coronavirus which infects humans and bats. It is an enveloped, positive-sense, single-stranded RNA virus which enters its host cell by binding to the APN receptor. Along with Human coro ...

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 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus previously had a ...

is similar to other Betacoronaviruses and is approximately 300–500 nucleotides long.

Gammacoronavirus 3′ UTR

Gammacoronavirus ''Gammacoronavirus'' (Gamma-CoV) is one of the four genera (''Alpha''-, '' Beta-'', ''Gamma-'', and '' Delta-'') of coronaviruses. It is in the subfamily ''Orthocoronavirinae'' of the family ''Coronaviridae''. They are enveloped, positive-sense ...

es 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.

References

{{DEFAULTSORT:Coronavirus 3' UTR Cis-regulatory RNA elements

Alphacoronavirus 3′ UTR

Betacoronavirus 3′ UTR

Gammacoronavirus 3′ UTR

Deltacoronavirus 3′ UTR

See also

References