IstR RNA
Encyclopedia
The TisB-IstR toxin-antitoxin system is the first known toxin-antitoxin system
which is induced by the SOS response
in response to DNA damage.
first identified in Escherichia coli
. There are two small RNAs encoded by the IstR locus
: IstR-1 and IstR-2, of which IstR-1 works as antitoxins against the toxic protein
TisB (toxicity-induced by SOS B) which is encoded by the neighbouring tisAB gene
. IstR-1 is a 75 nucleotide
transcript expressed constitutively throughout growth
, whereas IstR-2 is a 140 nucleotide transcript induced by Mitomycin C (MMC). Both genes are though to be regulated by LexA
.
Deletion analysis confirmed the function of IstR, E. coli strain K-12 could not grow in the absence of IstR when tisAB was present. Inserting IstR genes on a plasmid
allowed the bacteria to grow normally.Further studies showed that expression
of IstR-1 alone is enough to remedy the toxic effects of TisB. IstR-2 is not involved in the regulation of tisAB.
. TisB is responsible for conferring toxicity through suspected membrane
disruption. Upon translation of the tisB gene, a +1 inactive primary transcript mRNA is produced, which must be endonucleolytically processed 42 nucleotides from the 5' end to yield a +42 translationally competent mRNA. In the +42 form, the mRNA has a ribosome loading/standby site in an unstructured region >80 nt upstream of the tisB ribosome binding site, thus allowing translation of the TisB protein. This standby site is structurally unavailable in the inactive forms of the tisB mRNA (the +1 form and the +106 form produced by RNase III cleavage).
. Degradation results in a +106 form, an inactive 249 nt transcript which cannot be translated.
is to cause growth arrest, rather than cell death, in response to DNA damage, allowing time for repair processes to occur. TisB translation is under LexA control, so it is induced by DNA damage as part of the SOS response
. Under normal conditions, very little tisB mRNA is synthesised and translation is inhibited, but when DNA damage occurs tisAB is strongly induced causing overexpression, which overrides inhibition by depleting the IstR-1 pool. Experimental data has shown effects of TisB to be decreases in transcription, translation and replication, RNA degradation and ribosome disassembly. TisB does not affect transcription and translation directly in vitro, so these effects are thought to be downstream consequences of membrane damage.
TisB insertion into the membrane is thought to result in a loss of membrane potential. This could account for a decrease in ATP concentration in cells following triggering of the SOS response, causing slowing of cellular processes and inhibited cell growth.
Toxin-antitoxin system
A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid...
which is induced by the SOS response
SOS response
The SOS response is a global response to DNA damage in which the cell cycle is arrested and DNA repair and mutagenesis are induced. The SOS uses the RecA protein . The RecA protein, stimulated by single-stranded DNA, is involved in the inactivation of the LexA repressor thereby inducing the response...
in response to DNA damage.
IstR-1 and IstR-2
IstR sRNA (inhibitor of SOS-induced toxicity by RNA) is a family of non-coding RNANon-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...
first identified in Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
. There are two small RNAs encoded by the IstR locus
Locus (genetics)
In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...
: IstR-1 and IstR-2, of which IstR-1 works as antitoxins against the toxic 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...
TisB (toxicity-induced by SOS B) which is encoded by the neighbouring tisAB 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...
. IstR-1 is a 75 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...
transcript expressed constitutively throughout growth
Cell growth
The term cell growth is used in the contexts of cell development and cell division . When used in the context of cell division, it refers to growth of cell populations, where one cell grows and divides to produce two "daughter cells"...
, whereas IstR-2 is a 140 nucleotide transcript induced by Mitomycin C (MMC). Both genes are though to be regulated by LexA
Repressor lexA
Repressor LexA or LexA is a repressor enzyme that represses SOS response genes coding for DNA polymerases required for repairing DNA damage. LexA is intimately linked to RecA in the biochemical cycle of DNA damage and repair. RecA binds to DNA-bound LexA causing LexA to cleave itself in a...
.
Deletion analysis confirmed the function of IstR, E. coli strain K-12 could not grow in the absence of IstR when tisAB was present. Inserting IstR genes on a plasmid
Plasmid
In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...
allowed the bacteria to grow normally.Further studies showed that expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
of IstR-1 alone is enough to remedy the toxic effects of TisB. IstR-2 is not involved in the regulation of tisAB.
TisAB
The tisAB locus codes for two genes: tisA and tisB. The tisA reading frame was shown through a translation assay to not be translated. Its sequence is unconserved across species. TisB is a 29 amino acid peptide widely conserved in enterobacteriaEnterobacteriaceae
The Enterobacteriaceae is a large family of bacteria that includes many of the more familiar pathogens, such as Salmonella, Escherichia coli, Yersinia pestis, Klebsiella and Shigella. This family is the only representative in the order Enterobacteriales of the class Gammaproteobacteria in the...
. TisB is responsible for conferring toxicity through suspected membrane
Cell membrane
The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...
disruption. Upon translation of the tisB gene, a +1 inactive primary transcript mRNA is produced, which must be endonucleolytically processed 42 nucleotides from the 5' end to yield a +42 translationally competent mRNA. In the +42 form, the mRNA has a ribosome loading/standby site in an unstructured region >80 nt upstream of the tisB ribosome binding site, thus allowing translation of the TisB protein. This standby site is structurally unavailable in the inactive forms of the tisB mRNA (the +1 form and the +106 form produced by RNase III cleavage).
Mechanism of TisB inhibition by IstR-1
IstR-1 is thought to both inhibit translation of the TisB toxin, and promote RNase III cleavage of the RNA duplex formed when IstR-1 base pairs to tisB mRNA. Binding of the complimentary sequence of istR-1 sRNA to tisB mRNA in the ribosome standby site is thought to prevent loading of ribosomes and therefore prevent translation of the TisB protein. A RACE analysis confirmed that IstR-1 binds TisB mRNA and the duplex is then degraded by RNase IIIRNase III
RNase III enzymes specifically bind to and cleave double-stranded RNA . There are three subdivisions, known as Class 1, 2, and 3.Prokaryotic ribonuclease III is an enzyme that digests double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs.* Class 1...
. Degradation results in a +106 form, an inactive 249 nt transcript which cannot be translated.
Proposed function of the IstR-TisB toxin-antitoxin system
The proposed function of this toxin-antitoxin systemToxin-antitoxin system
A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid...
is to cause growth arrest, rather than cell death, in response to DNA damage, allowing time for repair processes to occur. TisB translation is under LexA control, so it is induced by DNA damage as part of the SOS response
SOS response
The SOS response is a global response to DNA damage in which the cell cycle is arrested and DNA repair and mutagenesis are induced. The SOS uses the RecA protein . The RecA protein, stimulated by single-stranded DNA, is involved in the inactivation of the LexA repressor thereby inducing the response...
. Under normal conditions, very little tisB mRNA is synthesised and translation is inhibited, but when DNA damage occurs tisAB is strongly induced causing overexpression, which overrides inhibition by depleting the IstR-1 pool. Experimental data has shown effects of TisB to be decreases in transcription, translation and replication, RNA degradation and ribosome disassembly. TisB does not affect transcription and translation directly in vitro, so these effects are thought to be downstream consequences of membrane damage.
TisB insertion into the membrane is thought to result in a loss of membrane potential. This could account for a decrease in ATP concentration in cells following triggering of the SOS response, causing slowing of cellular processes and inhibited cell growth.