The Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif (STAXI RNA motif) is a conserved
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 ...
-like structure identified using
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...
.
STAXI RNAs are located near to
gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
s encoding
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s that interact with
DNA (
Ssbp
Single-stranded binding proteins (SSBs) are a class of proteins that have been identified in both viruses and organisms from bacteria to humans.
Viral SSB
Although the overall picture of ''human cytomegalovirus'' (HHV-5) DNA synthesis appears ...
,
topoisomerase
DNA topoisomerases (or topoisomerases) are enzymes that catalyze changes in the topological state of DNA, interconverting relaxed and supercoiled forms, linked (catenated) and unlinked species, and knotted and unknotted DNA. Topological issues i ...
, XerDC
integrase
Retroviral integrase (IN) is an enzyme produced by a retrovirus (such as HIV) that integrates—forms covalent links between—its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage i ...
) or are associated with such proteins (
antirestriction proteins, which inhibit
restriction enzyme
A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class ...
s). This observation raised the possibility that instances of the STAXI motif function as single-stranded DNA molecules, perhaps during
DNA replication
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inherita ...
or
DNA repair
DNA repair is 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 radiation can cause DNA da ...
. On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG
tetraloop
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. There are many variants of the tetraloop. The published ones include ANYA,
CUYG,
GNRA,
UNAC
and UNCG.
Three types of tetraloops are ...
, but the DNA version of this tetraloop (TNCG) is not especially stable. The STAXI motif consists of a simple
pseudoknot
__NOTOC__
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 ...
structure that is repeated two or more times (see diagram).
A number of other RNAs were identified in the same study, including:
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Bacteroidales-1 RNA motif
The Bacteroidales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It has been identified only in bacteria within the order (biology) Bacteroidales. Its presumed length is marked by a promoter on one end that conforms to a ...
*
Chlorobi-1 RNA motif
The Chlorobi-1 RNA motif is a conserved RNA secondary structure identified by bioinformatics. It is predicted to be used only by Chlorobiota (formerly Chlorobi), a phylum of bacteria. The motif consists of two stem-loops that are followed by an ...
*
JUMPstart RNA motif
The 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. The ...
*
Lactis-plasmid RNA motif
The ''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 ...
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Ocean-V RNA motif
The 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
The ...
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potC RNA motif
The ''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. Thus, this RNA is present in environmen ...
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psaA RNA motif
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TwoAYGGAY RNA motif
The TwoAYGGAY RNA motif is a conserved RNA structure identified by bioinformatics. Its name refers to the conserved AYGGAY nucleotide sequence (Y refers to either a C or U nucleotide) found in the motif's two terminal loops (see diagram). The R ...
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ykkC-yxkD leader
The 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 for many years although it has been suggested that i ...
References
External links
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Non-coding RNA
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