Sib RNA refers to a group of related
non-coding RNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-c ...
. They were originally named QUAD RNA after they were discovered as four repeat elements in ''
Escherichia coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...
'' intergenic regions.
The family was later renamed Sib (for short intergenic abundant sequences) when it was discovered that the number of repeats is variable in other
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
and in other ''E. coli'' strains.
Identification
These small RNA were identified computationally by searching the genome of ''E. coli'' for
intergenic
An intergenic region is a stretch of DNA sequences located between genes. Intergenic regions may contain functional elements and Non-coding DNA#Junk DNA , junk DNA. ''Inter''genic regions should not be confused with ''intra''genic regions (or int ...
regions of high sequence identity (sequence conservation) with the genomes of closely related bacteria (several
salmonella
''Salmonella'' is a genus of rod-shaped (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two species of ''Salmonella'' are ''Salmonella enterica'' and ''Salmonella bongori''. ''S. enterica'' is the type species and is fur ...
species and ''
Klebsiella pneumoniae
''Klebsiella pneumoniae'' is a Gram-negative, non-motile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. It appears as a mucoid lactose fermenter on MacConkey agar.
Although found in the normal flora of the mouth ...
'').
This data was combined with
microarray
A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon t ...
expression analysis and potential novel ncRNAs identified. The expression of novel ncRNA of interest was confirmed by
northern blotting
The northern blot, or RNA blot,Gilbert, S. F. (2000) Developmental Biology, 6th Ed. Sunderland MA, Sinauer Associates. is a technique used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample.K ...
.
In this large scale screen these ncRNAs were simply referred to as candidates 43, 55 and 61.
These 3 ncRNA appear to be highly
homologous and are derived from a repeat region of the genome. Each of the ncRNA contains a short stretch homologous to boxC, a repeat element of unknown function present in 50 copies or more within the
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
of ''E. coli''.
Function
Sib RNA regulates the
expression
Expression may refer to:
Linguistics
* Expression (linguistics), a word, phrase, or sentence
* Fixed expression, a form of words with a specific meaning
* Idiom, a type of fixed expression
* Metaphorical expression, a particular word, phrase, o ...
of a toxic
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, respo ...
in a type I
toxin-antitoxin system
A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a "toxin" protein and a corresponding "antitoxin". Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in mult ...
similar to that of
hok/sok and''ldr-rdl'' genes.
The constitutively expressed ''Sib'' transcript regulates the ''ibs'' (induction brings stasis)
open reading frame
In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible readin ...
which encodes a small 18–19 amino acid
hydrophobic
In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water.
Hydrophobic molecules tend to be nonpolar and, th ...
protein which slows growth at moderate levels of expression and is toxic when overexpressed. The ''ibs'' gene is on the opposite strand to ''sib'' and is completely complementary, so the
antisense
In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, ...
-binding of Sib RNA with the ''ibs''
mRNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein.
mRNA is ...
brings about
dsRNA
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 ...
-mediated degradation.
When ''sib'' was
deleted in multi-copy
plasmids
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...
, the cells could not be maintained due to the toxicity of the unrepressed ''ibs'' protein. The toxicity mechanism of ibs protein is not fully understood, but a change in membrane potential upon over-expression of the protein suggests that interactions with
membrane protein
Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending on their location. Integral membrane proteins are a permanent part of a cell membrane ...
s or membrane insertion brings about
cell death
Cell death is the event of a biological cell ceasing to carry out its functions. This may be the result of the natural process of old cells dying and being replaced by new ones, as in programmed cell death, or may result from factors such as dis ...
.
See also
*
Addiction module Addiction modules are toxin-antitoxin systems. Each consists of a pair of genes that specify two components: a stable toxin and an unstable antitoxin that interferes with the lethal action of the toxin. Found first in E. coli on low copy number plas ...
*
TisB-IstR toxin-antitoxin system
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.
IstR-1 and IstR-2
IstR sRNA (inhibitor of SOS-induced toxicity by RNA) is a family of non-coding RNA fi ...
References
Further reading
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*
External links
* {{Rfam, id=RF00113, name=QUAD RNA
Antisense RNA
RNA antitoxins