STAXI RNA motif
Encyclopedia
The Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif (STAXI RNA motif) is a conserved RNA
-like structure identified using bioinformatics
. STAXI RNAs are located near to gene
s encoding protein
s that interact with DNA
(Ssbp
, topoisomerase
, XerDC integrase
) or are associated with such proteins (antirestriction proteins, which inhibit restriction enzyme
s). This observation raised the possibility that instances of the STAXI motif function as single-stranded DNA molecules, perhaps during DNA replication
or DNA repair
. On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG tetraloop
, but the DNA version of this tetraloop (TNCG) is not especially stable. The STAXI motif consists of a simple pseudoknot
structure that is repeated two or more times (see diagram).
A number of other RNAs were identified in the same study, including:
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
-like structure identified using bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
. STAXI RNAs are located near to gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s encoding protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s that interact with DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
(Ssbp
Single-strand binding protein
Single-strand binding protein, also known as SSB or SSBP, binds to single stranded regions of DNA to prevent premature annealing. The strands have a natural tendency to revert to the duplex form, but SSB binds to the single strands, keeping them separate and allowing the DNA replication machinery...
, topoisomerase
Topoisomerase
Topoisomerases are enzymes that regulate the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double helical structure. For example, during DNA replication, DNA becomes overwound ahead of a replication fork...
, XerDC integrase
Integrase
Retroviral integrase is an enzyme produced by a retrovirus that enables its genetic material to be integrated into the DNA of the infected cell...
) or are associated with such proteins (antirestriction proteins, which inhibit restriction enzyme
Restriction enzyme
A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...
s). This observation raised the possibility that instances of the STAXI motif function as single-stranded DNA molecules, perhaps during DNA replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
or DNA repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
. On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG tetraloop
Tetraloop
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG. The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3'...
, but the DNA version of this tetraloop (TNCG) is not especially stable. The STAXI motif consists of a simple pseudoknot
Pseudoknot
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982...
structure that is repeated two or more times (see diagram).
A number of other RNAs were identified in the same study, including:
- Bacteroidales-1 RNA motifBacteroidales-1 RNA motifThe Bacteroidales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It has been identified only in bacteria within the order Bacteroidales...
- Chlorobi-1 RNA motifChlorobi-1 RNA motifThe Chlorobi-1 RNA motif is a conserved RNA secondary structure identified by bioinformatics. It is predicted to be used only by Chlorobi, a phylum of bacteria. The motif consists of two stem-loops that are followed by an apparent rho-independent transcription terminator...
- JUMPstart RNA motifJUMPstart RNA motifThe JUMPstart RNA motif describes a conserved RNA-based secondary structure associated with JUMPstart elements. The 39-base-pair JUMPstart sequence describes a conserved element upstream of genes that participate in polysaccharide synthesis...
- Lactis-plasmid RNA motifLactis-plasmid RNA motifThe lactis-plasmid RNA motif is a conserved RNA structure identified by bioinformatics. The RNAs are restricted to lactic acid bacteria, and are especially common in Lactococcus lactis. They typically lie near to repB genes, and are almost found in plasmids. This data suggested that...
- Ocean-V RNA motifOcean-V RNA motifThe Ocean-V RNA motif is a conserved RNA structure discovered using bioinformatics. Only a few Ocean-V RNA sequences have been detected, all in sequences derived from DNA that was extracted from uncultivated bacteria found in ocean water. As of 2010, no Ocean-V RNA has been detected in any known,...
- PotC RNA motifPotC RNA motifThe potC RNA motif is a conserved RNA structure discovered using bioinformatics. The RNA is detected only in genome sequences derived from DNA that was extracted from uncultivated marine bacteria...
- PsaA RNA motifPsaA RNA motifThe psaA RNA motif describes a class of RNAs with a common secondary structure. psaA RNAs are exclusively found in locations that presumably correspond to the 5' untranslated regions of operons formed of psaA and psaB genes. For this reason, it was hypothesized that psaA RNAs function as...
- TwoAYGGAY RNA motifTwoAYGGAY RNA motifThe TwoAYGGAY RNA motif is a conserved RNA structure identified by bioinformatics. Its name refers to the conserved AYGGAY nucleotide sequence found in the motif's two terminal loops...
- YkkC-yxkD leaderYkkC-yxkD leaderThe YkkC/YxkD leader is a conserved RNA structure found upstream of the ykkC and yxkD genes in Bacillus subtilis and related genes in other bacteria. The function of this family is unclear although it has been suggested that it may function to switch on efflux pumps and detoxification systems in...