Bamboo mosaic virus satellite RNA cis-regulatory element

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Bamboo mosaic virus satellite RNA cis-regulatory element
RF00389.jpg
Predicted secondary structure and sequence conservation of satBaMV_CRE
Identifiers
SymbolsatBaMV_CRE
Rfam RF00389
Other data
RNA type Cis-reg
Domain(s) Viruses
SO 0000233
PDB structures PDBe

The bamboo mosaic virus satellite RNA cis-regulatory element is an RNA element found in the 5' UTR of the genome of the bamboo mosaic virus. This element is thought to be essential for efficient RNA replication. [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.

Genome entirety of an organisms hereditary information; genome of organism (encoded by the genomic DNA) is the (biological) information of heredity which is passed from one generation of organism to the next; is transcribed to produce various RNAs

In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA. The genome includes both the genes and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics.

Bamboo mosaic virus (BaMV) is a plant pathogenic virus in the genus Potexvirus and the family Alphaflexiviridae. BaMV is a filamentous, flexuous rod, 490 nm in length and 15 nm in width. The virus has been fully sequenced and it is 6366 nucleotides long.

Contents

See also

Bamboo mosaic potexvirus (BaMV) cis-regulatory element

The Bamboo mosaic potexvirus (BaMV) cis-regulatory element represents a cloverleaf-like cis-regulatory element found in the 3' UTR of the bamboo mosaic virus. This family is thought to play an important role in the initiation of minus-strand RNA synthesis and may also be involved in the regulation of viral replication.

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.

Poxvirus AX element late mRNA cis-regulatory element

The Poxvirus AX element late mRNA family represents a cis-regulatory element present at the 3' end of poxvirus late ATI mRNA and is known as the AX element. The AX element is involved in directing the efficient production and orientation-dependent formation of late RNAs. It is likely that this element directs the endonucleolytic cleavage of the transcript. It has been shown that the F17R late mRNA transcript which is also cleaved is also likely to share a common factor in their mechanism despite a lack of any obvious similarity in its cis-regulatory RNA element.

Related Research Articles

A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. Regulation of gene expression is an essential feature of all living organisms and viruses.

A satellite is a subviral agent composed of nucleic acid that depends on the co-infection of a host cell with a helper virus for its 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.

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.

Rubella virus 3 cis-acting element

The Rubella virus 3' cis-acting element RNA family represents a cis-acting element found at the 3' UTR in the rubella virus. This family contains three conserved step loop structures. Calreticulin (CAL), which is known to bind calcium in most eukaryotic cells, is able to specifically bind to the first stem loop of this RNA. CAL binding is thought to be related to viral pathogenesis and in particular arthritis which occurs frequently in rubella infections in adults and is independent of viral viability. All stem loop structures are thought to be important for efficient viral replication and deletion of stem loop three is known to be lethal.

Togavirus 5 plus strand cis-regulatory element

The Togavirus 5' plus strand cis-regulatory element is an RNA element which is thought to be essential for both plus and minus strand RNA synthesis.

Tombus virus defective interfering (DI) RNA region 3

Tombus virus defective interfering (DI) RNA region 3 is an important cis-regulatory region identified in the 3' UTR of Tombusvirus defective interfering particles (DI).

UPSK RNA

The Upstream pseudoknot (UPSK) domain is an RNA element found in the turnip yellow mosaic virus, beet virus Q, barley stripe mosaic virus and tobacco mosaic virus, which is thought to be needed for efficient transcription. Disruption of the pseudoknot structure gives rise to a 50% drop in transcription efficiency. This element acts in conjunction with the Tymovirus/Pomovirus tRNA-like 3' UTR element to enhance translation.

Potexvirus is a genus of pathogenic viruses in the order Tymovirales, in the family Alphaflexiviridae. Plants serve as natural hosts. There are currently 37 species in this genus including the type species Potato virus X. Diseases associated with this genus include: mosaic and ringspot symptoms. The genus name comes from the type species POTato Virus X).

Alphaflexiviridae is a family of viruses in the order Tymovirales. Plants and fungi serve as natural hosts. There are currently 51 species in this family, divided among 6 genera. Diseases associated with this family include: mosaic and ringspot symptoms.

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 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.

References

  1. ↑ Annamalai P, Hsu YH, Liu YP, Tsai CH, Lin NS (June 2003). "Structural and mutational analyses of cis-acting sequences in the 5'-untranslated region of satellite RNA of bamboo mosaic potexvirus". Virology. 311 (1): 229–39. doi:10.1016/S0042-6822(03)00178-8. PMID   12832220.

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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