Human parechovirus 1 (HPeV1) cis regulatory element (CRE)

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Human parechovirus 1 (HPeV1) cis regulatory element (CRE)
RF00499.jpg
Predicted secondary structure and sequence conservation of Parecho_CRE
Identifiers
SymbolParecho_CRE
Rfam RF00499
Other data
RNA type Cis-reg
Domain(s) Viruses
SO 0000233
PDB structures PDBe

The Human Parechovirus 1 cis regulatory element is an RNA element which is located in the 5'-terminal 112 nucleotides of the genome of human parechovirus 1 (HPeV1). The element consists of two stem-loop structures (SL-A and SL-B) together with a pseudoknot. Disruption of any of these elements impairs both viral replication and growth. [1]

Cis-regulatory elements (CREs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology.

Nucleotide biological molecules that form the building blocks of nucleic acids

Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are the building blocks of nucleic acids; they are composed of three sub unit molecules: a nitrogenous base, a five-carbon sugar, and at least one phosphate group.

Stem-loop intramolecular base-pairing pattern in RNA and also DNA

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, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions.

Contents

See also

Parechovirus is a genus of viruses in the family Picornaviridae. Humans, ferrets, and various rodents serve as natural hosts. The genus currently consists of four accepted species. Human parechoviruses may cause gastrointestinal or respiratory illness in infants, and have been implicated in cases of myocarditis and encephalitis.

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Picornavirus family of viruses

A picornavirus is a virus belonging to the family Picornaviridae, a family of viruses in the order Picornavirales. Vertebrates, including humans, serve as natural hosts. Picornaviruses are nonenveloped viruses that represent a large family of small, cytoplasmic, plus-strand RNA (~7.5kb) viruses with a 30-nm icosahedral capsid. Its genome does not have a lipid membrane. Picornaviruses are found in mammals and birds. There are currently 80 species in this family, divided among 35 genera. Notable examples are Enterovirus, Aphthovirus, Cardiovirus, and Hepatovirus genera. The viruses in this family can cause a range of diseases including paralysis, meningitis, hepatitis and poliomyelitis. Picornaviruses are in Baltimore IV class. Their genome single-stranded (+) sense RNA is what functions as mRNA after entry into the cell and all viral mRNA synthesized is of genome polarity. The mRNA encodes RNA dependent RNA polymerase. This polymerase makes complementary minus strands of RNA, then uses them as templates to make more plus strands. So, an overview of the steps in picornavirus replication are in order: attachment, entry, translation, transcription/genome replication, assembly and exit.

VPg is a protein that is covalently attached to the 5′ end of positive strand viral RNA and acts as a primer during RNA synthesis in a variety of virus families including Picornaviridae, Potyviridae and Caliciviridae. The primer activity of VPg occurs when the protein becomes uridylated, providing a free hydroxyl that can be extended by the virally encoded RNA-dependent RNA polymerase. For some virus families, VPg also has a role in translation initiation by acting like a 5' mRNA cap.

Cardiovirus cis-acting replication element

This family represents a Cardiovirus cis-acting replication element (CRE) which is located within the region encoding the capsid protein VP2 and is required for viral replication.

Citrus tristeza virus replication signal

The Citrus tristeza virus replication signal is a regulatory element involved in a viral replication signal which is highly conserved in citrus tristeza viruses. Replication signals are required for viral replication and are usually found near the 5' and 3' termini of protein coding genes. This element is predicted to form ten stem loop structures some of which are essential for functions that provide for efficient viral replication.

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 replication. The mechanism of cis-regulation is unclear, but this element is postulated to function in the plus-strand.

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.

Coronavirus SL-III cis-acting replication element

The coronavirus SL-III cis-acting replication element (CRE) is an RNA element that regulates defective interfering (DI) RNA replication.

Enterovirus 5 cloverleaf cis-acting replication element

The Enterovirus 5' cloverleaf cis-acting replication element is an RNA element found in the 5' UTR of Enterovirus genomes. The element has a cloverleaf like secondary structure and is known to be a multifunctional cis-acting replication element (CRE), required for the initiation of negative strand RNA synthesis.

Hepatitis C stem-loop IV

The Hepatitis C stem-loop IV is part of a putative RNA element found in the NS5B coding region. This element along with stem-loop VII, is important for colony formation, though its exact function and mechanism are unknown.

Hepatitis C virus cis-acting replication element

The Hepatitis C virus (HCV) cis-acting replication element (CRE) is an RNA element which is found in the coding region of the RNA-dependent RNA polymerase NS5B. Mutations in this family have been found to cause a blockage in RNA replication and it is thought that both the primary sequence and the structure of this element are crucial for HCV RNA replication.

Hepatitis C virus stem-loop VII

Hepatitis C virus stem-loop VII is a regulatory element found in the coding region of the RNA-dependent RNA polymerase gene, NS5B. Similarly to stem-loop IV, the stem-loop structure is important for colony formation, though its exact function and mechanism are unknown.

Potato virus X cis-acting regulatory element

The Potato virus X cis-acting regulatory element is a cis-acting regulatory element found in the 3' UTR of the Potato virus X genome. This element has been found to be required for minus strand RNA accumulation and is essential for efficient viral replication.

Rotavirus cis-acting replication element

This family represents a rotavirus cis-acting replication element (CRE) found at the 3'-end of rotavirus mRNAs. The family is thought to promote the synthesis of minus strand RNA to form viral dsRNA.

Human rhinovirus internal cis-acting regulatory element

Human rhinovirus internal cis-acting regulatory element (CRE) is a CRE from the human rhinoviruses. The CRE is located within the genome segment encoding the capsid proteins so is found in a protein coding region. The element is essential for efficient viral replication and it has been suggested that the CRE is required for initiation of minus-strand RNA synthesis.

Cis-acting replication elements bring together the 5' and 3' ends during replication of positive-sense single-stranded RNA viruses and double-stranded RNA viruses.

In molecular biology, the Hepatitis A virus cis-acting replication element (CRE) is an RNA element which is found in the coding region of the RNA-dependent RNA polymerase in Hepatitis A virus (HAV). It is larger than the CREs found in related Picornavirus species, but is thought to be functionally similar. It is thought to be involved in uridylylation of VPg.

In molecular biology, the Norovirus cis-acting replication element (CRE) is an RNA element which is found in the coding region of the RNA-dependent RNA polymerase in Norovirus. It occurs near to the 5' end of the RNA dependant RNA polymerase gene, this is the same location that the Hepatitis A virus cis-acting replication element is found in.

In molecular biology, the Avian encephalitis virus cis-acting replication element (CRE) is an s an RNA element which is found in the coding region of the RNA-dependent RNA polymerase in Avian encephalitis virus (AEV). It is structurally similar to the Hepatitis A virus cis-acting replication element.

References

  1. ↑ Nateri AS, Hughes PJ, Stanway G (December 2002). "Terminal RNA replication elements in human parechovirus 1". Journal of Virology. 76 (24): 13116–13122. doi:10.1128/JVI.76.24.13116-13122.2002. PMC   136667 . PMID   12438643.

Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families.

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