OLE RNA

Last updated
Ornate Large Extremophilic RNA
OLE secondary structure.jpg
Identifiers
SymbolOLE
Rfam RF01071
Other data
RNA type Gene
Domain(s) Bacteria
SO SO:0001263
PDB structures PDBe

OLE RNA (Ornate Large Extremophilic RNA) is a conserved RNA structure present in certain bacteria. [1] The RNA averages roughly 610 nucleotides in length. The only known RNAs that are longer than OLE RNA are ribozymes such as the group II intron and ribosomal RNAs. The exceptional length and highly conserved structure of OLE RNA prompted the hypothesis that OLE RNA could be a ribozyme, or otherwise perform an intricate biochemical task.

OLE RNAs are predominantly found in the order Clostridiales, but other kinds of Firmicutes contain OLE RNAs as well. Organisms containing OLE RNA are predominantly extremophiles and anaerobes.

OLE RNAs are transcribed as RNA, and experiments in Bacillus halodurans show that it is transcribed in a mRNA with 10 other genes. The adjacent genes are conserved in the vicinity of OLE RNA in most species containing it, but in Desulfitobacterium hafniense they are located elsewhere on the chromosome. OLE RNAs are processed from the larger transcript into a shorter RNA that roughly corresponds to the conserved, ~610-nucleotide structure. Genes encoding a protein class of unknown function are typically located immediately downstream of OLE RNAs, and the presence of this protein class is correlated in species with the presence of OLE RNA. This correlation suggests a possible functional association between the RNA and the protein.

X-ray structural studies revealed key elements that help specifically recognise the OapB protein in Bacillus halodurans. [2]

Related Research Articles

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RNA Family of large biological molecules

Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and DNA are nucleic acids. Along with lipids, proteins, and carbohydrates, nucleic acids constitute one of the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA, RNA is found in nature as a single strand folded onto itself, rather than a paired double strand. Cellular organisms use messenger RNA (mRNA) to convey genetic information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome.

<i>Paramyxoviridae</i>

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Ribozyme

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Riboswitch

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Transfer RNA RNA that facilitates the addition of amino acids to a new protein

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Ribosomal RNA RNA component of the ribosome, essential for protein synthesis in all living organisms

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Hammerhead ribozyme

The hammerhead ribozyme is an RNA motif that catalyzes reversible cleavage and ligation reactions at a specific site within an RNA molecule. It is one of several catalytic RNAs (ribozymes) known to occur in nature. It serves as a model system for research on the structure and properties of RNA, and is used for targeted RNA cleavage experiments, some with proposed therapeutic applications. Named for the resemblance of early secondary structure diagrams to a hammerhead shark, hammerhead ribozymes were originally discovered in two classes of plant virus-like RNAs: satellite RNAs and viroids. They have subsequently been found to be widely dispersed within many forms of life.

Hairpin ribozyme

The hairpin ribozyme is a small section of RNA that can act as a ribozyme. Like the hammerhead ribozyme it is found in RNA satellites of plant viruses. It was first identified in the minus strand of the tobacco ringspot virus (TRSV) satellite RNA where it catalyzes self-cleavage and joining (ligation) reactions to process the products of rolling circle virus replication into linear and circular satellite RNA molecules. The hairpin ribozyme is similar to the hammerhead ribozyme in that it does not require a metal ion for the reaction.

VS ribozyme

The Varkud satellite (VS) ribozyme is an RNA enzyme that carries out the cleavage of a phosphodiester bond.

Group I catalytic intron

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R2 RNA element

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The pistol ribozyme is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. The pistol ribozyme was discovered through comparative genomic analysis. Subsequent biochemical analysis determined further biochemical characteristics of the ribozyme. This understanding was further advanced by an atomic-resolution crystal structure of a pistol ribozyme

References

  1. Puerta-Fernandez E, Barrick JE, Roth A, Breaker RR (December 2006). "Identification of a large noncoding RNA in extremophilic eubacteria". Proc. Natl. Acad. Sci. U.S.A. 103 (51): 19490–19495. doi:10.1073/pnas.0607493103. PMC   1748253 . PMID   17164334.
  2. Yang, Yang; Harris, Kimberly A.; Widner, Danielle L.; Breaker, Ronald R. (2021-03-02). "Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex". Proceedings of the National Academy of Sciences. 118 (9): e2020393118. doi: 10.1073/pnas.2020393118 . ISSN   0027-8424.