RatA
Encyclopedia
RatA is a non-coding
222nt sRNA first identified in Bacillus subtilis
. It is part of a type-I toxin-antitoxin system along with the protein
toxin named TxpA (Toxic protein A).
RatA was discovered in intergenic regions of the B. subtilis genome
, in a 728-nucleotide
region between genes yqdB (later renamed TxpA) and yqbM. Initially, Affymetrix
microarrays
were used to detect transcription
in this region, Northern blot
experiments and mutation
analysis were then employed to characterise the RNA transcript.
ratA and txpA are transcribed convergently, and have an overlap of 75 base pairs at their [Directionality (molecular biology)#3' end|3' ends], providing an area of complimentarity. The RatA transcript binds with the TxpA mRNA across the complimentary region and the dsRNA is then degraded by an uncharacterised RNase E equivalent, preventing translation
of the toxic TxpA protein.
Gene
s ratA and txpA are found within a 48kb phage
-like element called skin. This element interrupts a gene for the sigma factor
σK and is excised during sporulation. The toxin-antitoxin system contained within skin forces the inheritance of this element, which is acting as a selfish gene
.
The mechanism by which TxpA induces cell lysis and death is unknown. TxpA is not similar enough to other proteins of known function to infer a related function, however it does have a suspected transmembrane region in its N-terminal, so it is possible that TxpA damages the integrity of the cell membrane, or blocks cell wall synthesis.
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
222nt sRNA first identified in Bacillus subtilis
Bacillus subtilis
Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium commonly found in soil. A member of the genus Bacillus, B. subtilis is rod-shaped, and has the ability to form a tough, protective endospore, allowing the organism to tolerate...
. It is part of a type-I toxin-antitoxin system along with the 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...
toxin named TxpA (Toxic protein A).
RatA was discovered in intergenic regions of the B. subtilis genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
, in a 728-nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
region between genes yqdB (later renamed TxpA) and yqbM. Initially, Affymetrix
Affymetrix
Affymetrix is a company that manufactures DNA microarrays; it is based in Santa Clara, California, United States. The company was founded by Dr. Stephen Fodor in 1992. It began as a unit in Affymax N.V...
microarrays
DNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
were used to detect transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
in this region, Northern blot
Northern blot
The northern blot is a technique used in molecular biology research to study gene expression by detection of RNA in a sample. With northern blotting it is possible to observe cellular control over structure and function by determining the particular gene expression levels during differentiation,...
experiments and mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...
analysis were then employed to characterise the RNA transcript.
ratA and txpA are transcribed convergently, and have an overlap of 75 base pairs at their [Directionality (molecular biology)#3' end|3' ends], providing an area of complimentarity. The RatA transcript binds with the TxpA mRNA across the complimentary region and the dsRNA is then degraded by an uncharacterised RNase E equivalent, preventing translation
Translation (genetics)
In molecular biology and genetics, translation is the third stage of protein biosynthesis . In translation, messenger RNA produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein...
of the toxic TxpA protein.
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 ratA and txpA are found within a 48kb phage
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
-like element called skin. This element interrupts a gene for the sigma factor
Sigma factor
A sigma factor is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. Different sigma factors are activated in response to different environmental conditions...
σK and is excised during sporulation. The toxin-antitoxin system contained within skin forces the inheritance of this element, which is acting as a selfish gene
Gene-centered view of evolution
The gene-centered view of evolution, gene selection theory or selfish gene theory holds that evolution occurs through the differential survival of competing genes, increasing the frequency of those alleles whose phenotypic effects successfully promote their own propagation, with gene defined as...
.
The mechanism by which TxpA induces cell lysis and death is unknown. TxpA is not similar enough to other proteins of known function to infer a related function, however it does have a suspected transmembrane region in its N-terminal, so it is possible that TxpA damages the integrity of the cell membrane, or blocks cell wall synthesis.