Bacterial small RNA
Encyclopedia
Bacterial small RNAs are small (50-250 nucleotide
) non-coding RNA
molecules produced by bacteria
, they are highly structured and contain several stem-loop
s. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as microarrays and Northern blotting in a number of bacterial species including Escherichia coli
, the nitrogen-fixing alpha-proteobacterium
Sinorhizobium meliloti
, marine cyanobacteria, Francisella tularensis
(the causative agent of tularaemia) and the plant pathogen Xanthomonas oryzae
pathovar oryzae.
In the 1960s, the abbreviation sRNA was used to refer to "soluble RNA," which is now known as transfer RNA
or tRNA (for an example of the abbreviation used in this sense, see .)
targets, and modify the function of the bound protein, or bind to mRNA targets and regulate gene expression
. Antisense sRNAs can be catagorised as cis-encoded sRNAs, where there is an overlap between the antisense sRNA and the target gene, and trans-encoded
sRNAs, where the antisense sRNA gene is separate from the target gene.
and regulates transcription
, tmRNA
has functions in protein synthesis, including the recycling of stalled ribosomes, 4.5S RNA regulates signal recognition particle (SRP)
, which is required for the secretion of proteins and RNase P
is involved in maturing tRNAs.
depeletion, onset of the SOS response
and sugar stress.
, a sigma factor
which regulates stress response and acts as a transcriptional regulator for many genes involved in cell adaptation. At least three sRNAs, DsrA, RprA and OxyS, regulate the translation of RpoS. DsrA and RprA both activate RpoS translation by base pairing to a region in the leader sequence of the RpoS mRNA and disrupting formation of a hairpin which frees up the ribosome loading site. OxyS inhibits RpoS translation. DsrA levels are increased in response to low temperatures and osmotic stress, and RprA levels are increased in response to osmotic stress and cell-surface stress, therefore increasing RpoS levels in response to these conditions. Levels of OxyS are increased in response to oxidative stress
, therefore inhibiting RpoS under these conditions.
and MicF
in response to stress conditions. The outer membrane protein OmpA
anchors the outer membrane to the murein layer of the periplasmic space
. Its expression is downregulated in the stationary phase of cell-growth. In E. coli the sRNA MicA depletes OmpA levels, in Vibrio cholerae
the sRNA VrrA
represses synthesis of OmpA in response to stress.
the InvR RNA represses synthesis of the major outer membrane protein
OmpD, and SgrS sRNA regulates the expression of the secreted effector protein SopD. In Staphylococcus aureus
, RNAIII regulates a number of genes involved in toxin
and enzyme
production and cell-surface proteins. The FasX and Pel sRNAs in Streptococcus pyogenes
are encoded in loci
associated with virulence. Pel RNA activates synthesis of surface-associated and secreted proteins.
species, the Qrr
sRNAs and the chaperone protein Hfq
are involved in the regulation of quorum sensing
. Qrr sRNAs regulate the expression of several mRNAs including the quorum-sensing master regulators LuxR and HapR.
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...
) non-coding RNA
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...
molecules produced by bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
, they are highly structured and contain several stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
s. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as microarrays and Northern blotting in a number of bacterial species including 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...
, the nitrogen-fixing alpha-proteobacterium
Alphaproteobacteria
Alphaproteobacteria is a class of Proteobacteria. Like all Proteobacteria, they are Gram-negative.-Characteristics:The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds , symbionts of plants and animals, and a group of pathogens, the...
Sinorhizobium meliloti
Sinorhizobium meliloti
Sinorhizobium meliloti is a Gram-negative nitrogen-fixing bacterium . It forms a symbiotic relationship with legumes from the genera Medicago, Melilotus and Trigonella, including the model legume Medicago truncatula. This symbiosis results in a new plant organ termed a root nodule. The S...
, marine cyanobacteria, Francisella tularensis
Francisella tularensis
Francisella tularensis is a pathogenic species of gram-negative bacteria and the causative agent of tularemia or rabbit fever. It is a facultative intracellular bacterium....
(the causative agent of tularaemia) and the plant pathogen Xanthomonas oryzae
Xanthomonas oryzae
Xanthomonas oryzae is a species of proteobacteria. The major host of the bacteria is rice .The species contains two pathovars which are non-European: Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv...
pathovar oryzae.
In the 1960s, the abbreviation sRNA was used to refer to "soluble RNA," which is now known as transfer RNA
Transfer RNA
Transfer RNA is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that is used in biology to bridge the three-letter genetic code in messenger RNA with the twenty-letter code of amino acids in proteins. The role of tRNA as an adaptor is best understood by...
or tRNA (for an example of the abbreviation used in this sense, see .)
Function
sRNAs can either bind to proteinProtein
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...
targets, and modify the function of the bound protein, or bind to mRNA targets and regulate gene 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...
. Antisense sRNAs can be catagorised as cis-encoded sRNAs, where there is an overlap between the antisense sRNA and the target gene, and trans-encoded
Trans-acting
In the field of molecular biology, trans-acting , in general, means "acting from a different molecule"...
sRNAs, where the antisense sRNA gene is separate from the target gene.
House-keeping
Amongst the targets of sRNAs are a number of house-keeping genes. The 6S RNA binds to RNA polymeraseRNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
and regulates 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...
, tmRNA
TmRNA
Transfer-messenger RNA is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex together with Small Protein B , Elongation Factor Tu , and ribosomal protein S1...
has functions in protein synthesis, including the recycling of stalled ribosomes, 4.5S RNA regulates signal recognition particle (SRP)
Signal recognition particle
The signal recognition particle is an abundant, cytosolic, universally conserved ribonucleoprotein that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes....
, which is required for the secretion of proteins and RNase P
RNase P
Ribonuclease P is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA...
is involved in maturing tRNAs.
Stress response
Many sRNAs are involved in stress response regulation. They are expressed under stress conditions such as cold shock, ironIron
Iron is a chemical element with the symbol Fe and atomic number 26. It is a metal in the first transition series. It is the most common element forming the planet Earth as a whole, forming much of Earth's outer and inner core. It is the fourth most common element in the Earth's crust...
depeletion, onset 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...
and sugar stress.
Regulation of RpoS
The RpoS gene in E. coli encodes sigma 38Sigma 38
Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. The gene rpoS encodes sigma-38 , a 37.8 kD protein in Escherichia coli. rpoS is transcribed in late exponential phase, and RpoS is the primary...
, a 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...
which regulates stress response and acts as a transcriptional regulator for many genes involved in cell adaptation. At least three sRNAs, DsrA, RprA and OxyS, regulate the translation of RpoS. DsrA and RprA both activate RpoS translation by base pairing to a region in the leader sequence of the RpoS mRNA and disrupting formation of a hairpin which frees up the ribosome loading site. OxyS inhibits RpoS translation. DsrA levels are increased in response to low temperatures and osmotic stress, and RprA levels are increased in response to osmotic stress and cell-surface stress, therefore increasing RpoS levels in response to these conditions. Levels of OxyS are increased in response to oxidative stress
Oxidative stress
Oxidative stress represents an imbalance between the production and manifestation of reactive oxygen species and a biological system's ability to readily detoxify the reactive intermediates or to repair the resulting damage...
, therefore inhibiting RpoS under these conditions.
Regulation of outer membrane proteins
The outer membrane of gram negative bacteria acts as a barrier to prevent the entry of toxins into the bacterial cell, and plays a role in the survival of bacterial cells in diverse environments. Outer membrane proteins (OMPs) include porins and adhesins. Numerous sRNAs regulate the expression of OMPs. The porins OmpC and OmpF are responsible for the transport of metabolites and toxins. The expression of OmpC and OmpF is regulated by the sRNAs MicCMicC RNA
The MicC non-coding RNA is located between the ompN and ydbK genes in E. coli. This RNA is thought to be a regulator of the expression level of the OmpC porin protein, with a 5' region of 22 nucleotides potentially forming an antisense interaction with the ompC mRNA...
and MicF
MicF RNA
The micF RNA is a non-coding RNA stress response gene found in Escherichia coli and related bacteria that post-transcriptionally controls expression of the outer membrane porin gene ompF. The micF gene encodes a non-translated 93 nucleotide antisense RNA that binds its target ompF mRNA and...
in response to stress conditions. The outer membrane protein OmpA
OmpA-like transmembrane domain
OmpA-like transmembrane domain is an evolutionarily conserved domain of outer membrane proteins. This domain consists of an eight-stranded beta barrel. OmpA is the predominant cell surface antigen in enterobacteria found in about 100,000 copies per cell. The expression of OmpA is tightly regulated...
anchors the outer membrane to the murein layer of the periplasmic space
Periplasmic space
The periplasmic space or periplasm is a space between the peptidoglycan cell wall and inner membrane of Gram-negative bacteria or the equivalent space outside the inner membrane of Gram-positive bacteria. It may constitute up to 40% of the total cell volume in Gram-negative species, and is...
. Its expression is downregulated in the stationary phase of cell-growth. In E. coli the sRNA MicA depletes OmpA levels, in Vibrio cholerae
Vibrio cholerae
Vibrio cholerae is a Gram-negative, comma-shaped bacterium. Some strains of V. cholerae cause the disease cholera. V. cholerae is facultatively anaerobic and has a flagella at one cell pole. V...
the sRNA VrrA
Vibrio regulatory RNA of OmpA
VrrA is a non-coding RNA that is conserved across all Vibrio species of bacteria and acts as a repressor for the synthesis of the outer membrane protein OmpA...
represses synthesis of OmpA in response to stress.
Virulence
In some bacteria sRNAs regulate virulence genes. In SalmonellaSalmonella
Salmonella is a genus of rod-shaped, Gram-negative, non-spore-forming, predominantly motile enterobacteria with diameters around 0.7 to 1.5 µm, lengths from 2 to 5 µm, and flagella which grade in all directions . They are chemoorganotrophs, obtaining their energy from oxidation and reduction...
the InvR RNA represses synthesis of the major outer membrane protein
Virulence-related outer membrane protein family
Virulence-related outer membrane proteins are expressed in Gram-negative bacteria and are essential to bacterial survival within macrophages and for eukaryotic cell invasion.This family consists of several bacterial and phage Ail/Lom-like proteins....
OmpD, and SgrS sRNA regulates the expression of the secreted effector protein SopD. In Staphylococcus aureus
Staphylococcus aureus
Staphylococcus aureus is a facultative anaerobic Gram-positive coccal bacterium. It is frequently found as part of the normal skin flora on the skin and nasal passages. It is estimated that 20% of the human population are long-term carriers of S. aureus. S. aureus is the most common species of...
, RNAIII regulates a number of genes involved in toxin
Toxin
A toxin is a poisonous substance produced within living cells or organisms; man-made substances created by artificial processes are thus excluded...
and enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
production and cell-surface proteins. The FasX and Pel sRNAs in Streptococcus pyogenes
Streptococcus pyogenes
Streptococcus pyogenes is a spherical, Gram-positive bacterium that is the cause of group A streptococcal infections. S. pyogenes displays streptococcal group A antigen on its cell wall. S...
are encoded in loci
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...
associated with virulence. Pel RNA activates synthesis of surface-associated and secreted proteins.
Quorum sensing
In VibrioVibrio
Vibrio is a genus of Gram-negative bacteria possessing a curved rod shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in saltwater, Vibrio are facultative anaerobes that test positive for oxidase and do not form...
species, the Qrr
Qrr RNA
Qrr is a non-coding RNA that is thought to be involved in the regulation of quorum sensing in Vibrio species. It is believed that these RNAs, guided by a protein, Hfq, can mediate the destabilisation of the quorum-sensing master regulators LuxR/HapR/VanT mRNAs.Qrr operates as part of a negative...
sRNAs and the chaperone protein Hfq
Hfq protein
The Hfq protein encoded by the hfq gene was discovered in 1968 as an Escherichia. coli host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial RNA binding protein which has many important physiological roles. Usually mediated by...
are involved in the regulation of quorum sensing
Quorum sensing
Quorum sensing is a system of stimulus and response correlated to population density. Many species of bacteria use quorum sensing to coordinate gene expression according to the density of their local population. In similar fashion, some social insects use quorum sensing to determine where to nest...
. Qrr sRNAs regulate the expression of several mRNAs including the quorum-sensing master regulators LuxR and HapR.
See also
- Escherichia coli sRNAEscherichia coli sRNAEscherichia coli contains a number of small RNAs located in intergenic regions of its genome. The presence of at least 55 of these has been verfied experimentally. 275 potential sRNA-encoding loci were identified computationally using the QRNA program. These loci will include false positives, so...
- Mycobacterium tuberculosis sRNAMycobacterium tuberculosis sRNAMycobactierum tuberculosis contains at least nine small RNA families in its genome. The small RNA families were identified through RNomics - the direct analysis of RNA molecules isolated from cultures of Mycobacterium tuberculosis. The sRNAs were characterised through RACE mapping and Northern...
- Bacillus subtilis BSR sRNAsBacillus subtilis BSR sRNAsIn a screen of the Bacillus subtilis genome for genes encoding ncRNAs, Saito et al. focused on 123 intergenic regions over 500 bp in length, the authors analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt...
- Non-coding RNANon-coding RNAA 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...
- Xanthomonas sRNAXanthomonas sRNAIn molecular biology, Xanthomonas sRNA are small RNAs which have been identified in various species of the bacterium Xanthomonas.Analysis of the plant pathogen Xanthomonas campestris pv. vesicatoria revealed expression of seven cis-encoded antisense RNAs and 15 intergenic sRNAs...