The gene ''rpoS'' (RNA polymerase, sigma S, also called katF) encodes the
sigma factor
A sigma factor (σ factor or specificity factor) is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is ho ...
''sigma-38'' (σ38, or RpoS), a 37.8 kD protein 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 ...
''.
Sigma factors are proteins that regulate
transcription
Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including:
Genetics
* Transcription (biology), the copying of DNA into RNA, the fir ...
in
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
. Sigma factors can be activated in response to different environmental conditions. ''rpoS'' is transcribed in late exponential phase, and RpoS is the primary regulator of stationary phase genes. RpoS is a central regulator of the general stress response and operates in both a retroactive and a proactive manner: it not only allows the cell to survive environmental challenges, but it also prepares the cell for subsequent stresses (cross-protection).
The transcriptional regulator
CsgD
CsgD is a transcription and response regulator protein referenced to as the master modulator of bacterial biofilm development. In '' E. coli'' cells, CsgD is tasked with aiding the transition from planktonic cell motility to the stationary phase ...
is central to
biofilm
A biofilm comprises any syntrophic consortium of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular ...
formation, controlling the expression of the
curli
The Curli protein is a type of amyloid fiber produced by certain strains of enterobacteria. They are extracellular fibers located on bacteria such as ''E. coli'' and ''Salmonella'' spp. These fibers serve to promote cell community behavior throu ...
structural and export proteins, and the
diguanylate cyclase, adrA, which indirectly activates cellulose production.
The ''rpoS'' gene most likely originated in the
gammaproteobacteria
Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genera-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically imp ...
.
Environmental signal to activation: regulation of RpoS
Regulatory mechanisms that control RpoS exist at various levels of gene and protein organization:
transcription
Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including:
Genetics
* Transcription (biology), the copying of DNA into RNA, the fir ...
,
translation
Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...
, degradation, and protein activity. These processes occur in response to stresses such as near-
UV radiation
Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nm (with a corresponding frequency around 30 PHz) to 400 nm (750 THz), shorter than that of visible light, but longer than X-rays. UV radiation i ...
,
acid
In computer science, ACID ( atomicity, consistency, isolation, durability) is a set of properties of database transactions intended to guarantee data validity despite errors, power failures, and other mishaps. In the context of databases, a sequ ...
, temperature or
osmotic shock
Osmotic shock or osmotic stress is physiologic dysfunction caused by a sudden change in the solute concentration around a cell, which causes a rapid change in the movement of water across its cell membrane. Under hypertonic conditions - conditions ...
,
oxidative stress
Oxidative stress reflects an imbalance between the systemic manifestation of reactive oxygen species and a biological system's ability to readily Detoxification, detoxify the reactive intermediates or to repair the resulting damage. Disturbances ...
, and nutrient deprivation. While many key regulatory entities have been identified in these areas, the precise mechanisms by which they signal ''rpoS'' transcription, translation, proteolysis or activity remain largely uncharacterized.
Transcriptional control of ''rpoS''
Transcription of ''rpoS'' in ''E. coli'' is mainly regulated by the chromosomal rpoSp promoter.
rpoSp promotes transcription of ''rpoS'' mRNA, and is induced upon entry into
stationary phase in cells growing on rich media via an unknown mechanism. Flanking rpoSp are two putative
cAMP
Camp may refer to:
Outdoor accommodation and recreation
* Campsite or campground, a recreational outdoor sleeping and eating site
* a temporary settlement for nomads
* Camp, a term used in New England, Northern Ontario and New Brunswick to descri ...
-CRP (cyclic AMP-cAMP
receptor protein) binding sites that seem to control ''rpoS'' transcription in an antagonistic manner. The position of the first site upstream of the major ''rpoS'' promoter corresponds to a “classical activator” similarly found in the ''
lac
Lac is the resinous secretion of a number of species of lac insects, of which the most commonly cultivated is ''Kerria lacca''.
Cultivation begins when a farmer gets a stick that contains eggs ready to hatch and ties it to the tree to be infes ...
'' promoter thereby suggesting that its effects on transcription are activating (Lange and Hengge-Aronis, 1994); in contrast, the location of the second cAMP-CRP site is indicative of inhibitory action. In exponential phase, ''crp'' mutants exhibit high levels of ''rpoS'' expression, suggesting that cAMP-CRP inhibits ''rpoS'' transcription. Upon entry into stationary phase, on the other hand, cAMP-CRP may upregulate ''rpoS'' transcription (Hengge-Aronis, 2002). While these observations may explain the seemingly dual nature of the cAMP-CRP binding sites, they require an explanation of phase-dependent selection of cAMP-CRP site activation to fully account for the contradictory data. Additional regulatory controls for ''rpoS'' transcription include: BarA, a
Histidine sensor kinase
In biochemistry, a kinase () is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule don ...
which can activate OmpR and thereby promote porin synthesis; levels of small molecules such as
ppGppp which may hinder transcriptional elongation or stability in response to amino acid limitation, or carbon, nitrogen or phosphorus starvation (Gentry ''et al.'', 1993). Despite the numerous controls on ''rpoS'' transcription, cellular ''rpoS'' mRNA levels remain high during exponential phase and the majority of extracellular
stimuli
A stimulus is something that causes a physiological response. It may refer to:
* Stimulation
** Stimulus (physiology), something external that influences an activity
** Stimulus (psychology), a concept in behaviorism and perception
* Stimulus (eco ...
do not significantly affect ''rpoS'' transcription.
Translational control of ''rpoS''
Most RpoS expression is determined at the translational level.
sRNAs (small noncoding
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 ...
s) sense environmental changes and in turn increase ''rpoS'' mRNA translation to allow the cell to accordingly adjust to external stress. The promoter of the 85 nucleotide sRNA
DsrA contains a temperature-sensitive transcription initiation thermocontrol as it is repressed at high (42˚C) temperatures, but induces (perhaps by complementary binding to) ''rpoS'' at low (25˚C) temperatures.
Another sRNA,
RprA, stimulates ''rpoS'' translation in response to cell surface stress signaled via the RcsC
sensor kinase.
A third type of sRNA, OxyS, is regulated by OxyR, the primary sensor of oxidative shock. The mechanism by which OxyS interferes with ''rpoS'' mRNA
translational efficiency is not known. However, the RNA-binding protein
Hfq is implicated in the process. Hfq binds to ''rpoS'' mRNA ''
in vitro
''In vitro'' (meaning in glass, or ''in the glass'') studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in biology an ...
'' and may thereby modify ''rpoS'' mRNA structure for optimal translation. Hfq activates both DsrA and RprA. In contrast, LeuO inhibits ''rpoS'' translation by repressing ''dsrA'' expression and the histone-like protein HN-S (and its paralog StpA) inhibits ''rpoS'' translation via an unknown mechanism. In addition, H-NS, LeuO, Hfq and DsrA form an interconnected regulatory network that ultimately controls ''rpoS'' translation.
RpoS translation was also shown to be controlled in other bacterial species, beside Escherichia coli. E.g., in the opportunistic human pathogen
Pseudomonas aeruginosa
''Pseudomonas aeruginosa'' is a common encapsulated, gram-negative, aerobic–facultatively anaerobic, rod-shaped bacterium that can cause disease in plants and animals, including humans. A species of considerable medical importance, ''P. aerugi ...
the sRNA ReaL translationally silences rpoS mRNA.
RpoS degradation
RpoS proteolysis forms another level of the sigma factor’s regulation. Degradation occurs via ClpXP, a barrel-shaped protease composed of two six-subunit rings of the ATP-dependent ClpX chaperone that surround two seven-subunit rings of ClpP (Repoila ''et al.'', 2003). The response regulator RssB has been identified as a σS-specific recognition factor crucial for RpoS degradation. Additional factors known to regulate RpoS proteolysis but via incompletely characterized mechanisms include: RssA which is found on the same operon as RssB; H-NS and DnaK, both of which also regulate ''rpoS'' mRNA translation, and LrhA; and acetyl phosphate affects RpoS proteolysis by possibly acting as a phosphoryl donor to RssB.
The RpoS regulon
Consistent with its role as the master controller of the bacterial stress response, RpoS regulates the expression of stress-response genes that fall into various functional categories: stress resistance, cell morphology,
metabolism
Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...
,
virulence
Virulence is a pathogen's or microorganism's ability to cause damage to a host.
In most, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its ability to ca ...
and
lysis
Lysis ( ) is the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic (that is, "lytic" ) mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a ''lysate''. In molecular bio ...
.
Stress resistance
Many genes under RpoS control confer stress resistance to assaults such as
DNA damage
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 ...
, presence of
reactive oxygen species
In chemistry, reactive oxygen species (ROS) are highly reactive chemicals formed from diatomic oxygen (). Examples of ROS include peroxides, superoxide, hydroxyl radical, singlet oxygen, and alpha-oxygen.
The reduction of molecular oxygen () p ...
and
osmotic shock
Osmotic shock or osmotic stress is physiologic dysfunction caused by a sudden change in the solute concentration around a cell, which causes a rapid change in the movement of water across its cell membrane. Under hypertonic conditions - conditions ...
. The product of ''xthA'' is an exonuclease that participates in DNA repair by recognizing and removing 5’ monophosphates near abasic sites in damaged DNA. Likewise, catalases HPI and HPII, encoded by ''katG'' and ''katE'' convert harmful hydrogen peroxide molecules to water and oxygen. The ''otsBA'' gene product
trehalose
Trehalose (from Turkish '' tıgala'' – a sugar derived from insect cocoons + -ose) is a sugar consisting of two molecules of glucose. It is also known as mycose or tremalose. Some bacteria, fungi, plants and invertebrate animals synthesize it ...
functions as an
osmoprotectant
Osmoprotectants or compatible solutes are small organic molecules with neutral charge and low toxicity at high concentrations that act as osmolytes and help organisms survive extreme osmotic stress. Osmoprotectants can be placed in three chemical c ...
and is needed for desiccation resistance. Additional RpoS-dependent factors involved in oxidative stress include
glutathione reductase
Glutathione reductase (GR) also known as glutathione-disulfide reductase (GSR) is an enzyme that in humans is encoded by the GSR gene. Glutathione reductase (EC 1.8.1.7) catalyzes the reduction of glutathione disulfide ( GSSG) to the sulfhydryl f ...
(encoded by ''gor''), and
superoxide dismutase
Superoxide dismutase (SOD, ) is an enzyme that alternately catalyzes the dismutation (or partitioning) of the superoxide () radical into ordinary molecular oxygen (O2) and hydrogen peroxide (). Superoxide is produced as a by-product of oxygen me ...
(encoded by ''sodC'').
It has also been found, using comparative proteomic analysis with ''B. pseudomallei'', that rpoS regulates eight oxidative responsive proteins including ScoA (a SCOT subunit) not previously known for oxidative stress response involvement. The regulatory effect in this case is RpoS down regulation of SCOT expression in response to oxidative stress in ''B. pseudomallei''.
Morphology
RpoS-dependent genes involved in changes in cell membrane permeability and general cell morphology mostly belong to the ''osm'' family of genes. ''osmB'' encodes an outer membrane lipoprotein that may play a role in cell aggregation (Jung ''et al.'', 1990)
,
whereas ''osmY'' encodes a periplasmic protein. Additional RpoS-dependent factors that determine the size and shape of the cell include the morphogene ''bolA'' and products of the ''ftsQAZ'' operon that play a role in the timing of cell division.
Control of cell shape, cell division and cell-cell interaction are likely to be important in inhibiting cell proliferation and thus allocating resources to cell survival during periods of stress.
Metabolism
Metabolically-optimal survival conditions include RpoS-dependent decreased
Krebs cycle
The citric acid cycle (CAC)—also known as the Krebs cycle or the TCA cycle (tricarboxylic acid cycle)—is a series of chemical reactions to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and protein ...
activity and increased glycolytic activity to limit the reactive oxygen species that are byproduced as a result of essential cellular processes.
Pyruvate
Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell.
Pyruvic aci ...
entry into the Krebs cycle is inhibited by the product of the RpoS-dependent gene ''poxB''. An overall slowdown in metabolic activity is consistent with energy conservation and reduced growth during periods of stress.
Virulence
As a defense mechanism, the host environment is hostile to invading pathogens. Therefore, infection can be a stressful event for pathogenic bacteria and control of virulence genes may be temporally correlated with the timing of infection by pathogens. Discovery of RpoS-dependent virulence genes in ''Salmonella'' is consistent with RpoS as a general regulator of the stress response: the ''spv'' gene found on a virulence plasmid in this bacterium is controlled by RpoS and is required for growth in deep lymphoid tissue such as the spleen and liver.
Lysis
RpoS also plays an important role in regulating cell lysis. Along with OmpR, it upregulates the
entericidin (''ecnAB'') locus which encodes a lysis-inducing toxin.
In contrast, ''ssnA'' is negatively controlled by RpoS but it also promotes lysis. Paradoxically, lysis is seen as a survival process in certain contexts.
References
Further reading
*
*
{{Escherichia coli
Escherichia coli genes