The Escherichia coli SOS response is an inducible DNA damage repair pathway controlled by two key regulators, LexA, a repressor and RecA, an inducer. Upon DNA damage RecA is activated and stimulates self cleavage of LexA, leading to, in E. coli, derepresion of approximately 50 SOS genes. The response is triggered by exogenous and endogenous signals that bacteria encounter at a number of sites within the host. Nevertheless, besides regulating DNA damage repair the SOS response plays a much broader role. Thus, SOS error prone polymerases promote elevated mutation rates significant for genetic adaptation and diversity, including antibiotic resistance. Here we review the E. coli SOS response in relation to recalcitrance to antimicrobials, including persister and biofilm formation, horizontal gene tranfer, gene mobility, bacterial pathogenicity, as well SOS induced bacteriocins that drive diversification. Phenotypic heterogeneity in expression of the SOS regulator genes, recA and lexA as well as colicin activity genes is also discussed.
- SOS response
- Escherichia coli
- DNA damage
- antibiotic resistance
- horizontal gene transfer
- phentypic heterogeneity
Bacteria are constantly exposed to a changing and stressful environment. Coordinated responses by bacterial global regulatory systems enable their survival and adaptation .
In all organisms genome integrity is constantly threatened by endogenous and exogenous agents. Exogenous DNA damaging agents are physical (UV and ionizing irradiation, oxidants, drugs) and chemical (oxidizing, crosslinking, alkylating). Endogenous triggers are the result of cellular metabolism such as reactive oxygen species (ROS), stalled replication forks and defects following recombination or chromosome segregation [2, 3]. To cope with DNA damage organisms possess a number of error free and error prone mechanisms [4, 5]. Most bacteria seem to have evolved a coordinated response to DNA damage. In
Even though RecA and LexA are the key SOS regulators, induction/SOS factors may also be governed by other stress response pathways namely, alternative sigma factors RpoS and RpoH of the general stress responses, the stringent response, cAMP and reactive oxgen species (ROS) [6, 7, 8, 9, 10].
Whilst the SOS response was initially recognized as regulating DNA damage repair, it is now well established that it plays’ a much broader role. Thus, SOS error prone polymerases by promoting elevated mutation rates generate genetic diversity and adaptation. The SOS response is also involved in horizontal gene transfer, virulence factor expression, biofilms, persistence, sustained colonization of the mammalian gut, controls toxin-antitoxin systems as well as intraspecies competition and phenotypic variation (Figure 1) [5, 11, 12].
2. Mutagenesis and antibiotic resistance
Antibiotic resistance is one of the most serious global health threats. Resistance occurs by mutation of resident genes or/and by uptake of resistance genes. Antibiotic resistance mechanisms belong to one of several classes with resistance genes encoded on chromosomes and mobile genetic elements such as plasmids, transposons and integrons. As stated above, the error prone translesion DNA polymerases PolII, PolIV and PolV allow translesion DNA replication but also promote an increased level of mutation, significant for evolution of antibiotic resistance.
Exposure of bacteria to antibiotics, even at subinhibitory concentrations, has been shown to increase mutation and recombination frequencies via the SOS response [13, 14]. In
In addition to antibiotic resistance other mechanisms allow bacterial growth in the presence of antibiotics; (i) population wide tolerance, (ii) persisters, subpopulations characterized by a transient dormant state and transient tolerance  and (iii) shielding that protects and enables survival in the presence of antibiotics .
Persisters and antimicrobial tolerance have been extensively studied in
Recently, sub-inhibitory concentrations of ciprofloxacin were shown to, in
3. Mobile genetic elements
Horizontal gene transfer is a significant driving force of bacterial genome evolution, including the emergence and dissemination of antibiotic resistance and virulence genes. The SOS response has been shown to play an important role in gene transfer in a number of bacterial species.
One of the first reports of the involvement of the SOS response in horizontal gene transfer was SOS induction of transfer of antibiotic resistances encoded by the
An important class of SOS controlled mobile genetic elements are the wide spread integrons. They are associated particularly with transposons and conjugative plasmids and have played an important role in the evolution of antibiotic resistance among pathogenic bacteria . Integrons encode a site specific recombination system that promotes integration and expression of gene cassettes with antibiotic resistance and metabolism associated functions.
On the basis of integrase sequences, five classes of integrons are distinguished. Class 1 integrons are by far the most prevalent and clinically relevant. Recently, the class 1 integrons were found in a considerable fraction of
Integrons are composed of an
Integrons enable bacteria to evolve in response to new antibiotic challenges via rapid optimization of cassette expression. Activity of the integrase allows: (i) modulation of cassette expression, (ii) rapid gain of additional copies of selected cassettes and (iii) elimination of redundant cassettes. Integrase activity does not compromise genome integrity due to the high specificity of integrase-mediated recombination [32, 33, 34]. Thus, integrase-mediated cassette re-shuffling in stressful environments could accelerate bacterial evolution allowing bacteria to optimize cassette expression and maximize fitness. Relavant cassettes could be positioned near the Pc promoter for maximal expression, while unnecessary cassettes could be kept at the end of the array and be moved forward when required .
DNA acquired by HGT, including pathogenicity islands (PAIs) with virulence factor genes, must either replicate autonomously or be integrated into the bacterial chromose or plasmid. Integration is mediated by recombinases/integrases that are often encoded on PAIs and perform either integration or excision from the chromosome. It was recently shown that SOS inducing antibiotics, including clinically relevant for treatment of UTI, led to in a subpopulation, increased promoter activity as well as increased loss of PAIs .
To provoke UTI, UPEC undergo a complex intracellular cycle  and the SOS response plays an important role in bacterial dissemination and persistence within the urinary tract. UPEC enter the urinary tract through an ascending route and travel up the urethra to colonize the bladder via internalization by the umbrella cells. Infected cells produce nitric oxide that attacks bacterial DNA, inducing the SOS response with inhibition of cell division and UPEC filamentation. Filamentous UPEC successfully resist phagocyte killing, allowing dissemination and persistence within the urinary tract. UTI frequently lead to chronic infection and a persister subpopulation could be responsible for generating relapsing infections .
In the intestinal tract, DNA damage and subsequent SOS induction, can be provoked by host factors, e.g. bile salts, and by competing microbes. Intestinal inflammation triggered by infection or the gut immune system involving ROS, also induces the SOS response.
All EHEC strains, including the notorius serotype O157;H7, produce Stx the main virulence factor associated with hemorrhagic colitis .
Production of Stx, by O157:H7 is mediated by quorum sensing  however, it is also well documented that the SOS response amplifies Shiga toxin production in enterohemorrhagic
Thus, a strain producing the nuclease colicin E9 (ColE9) as well as extracted DNase colicins were shown to induce Stx . Recently, microcin B17 (MccB17), a DNA gyrase inhibitor, as well as a putative microcin, were also shown to amplify Stx
2a production [51, 52]. Thus in the gut, nonpathogenic
In addition to DNA damage induced by host factors, e.g. bile salts, and by competing microbes, intestinal inflammation triggered by infection or the gut immune system involving ROS, also provokes the SOS response and dysbiosis, suppressing anaerobes and inciting
Biofilms are surface attached structured bacterial communities that create a protective environment for bacterial cells . Biofilm formation is a highly regulated process and is controlled by a number of environmental and genetic factors [55, 56, 57]. Biofilms are also induced by antimicrobial stress/SOS response. While biofilm formation is an integral part of the prokaryotic life cycle, biofilms also cause biofilm associated diseases that are difficult to treat, e.g. urinary tract infections (UTI), chronic infections in cystic fibrosis (CF) patients, colonization of medical devices and periodontal diseases .
A number of factors allow bacteria in biofilms to survive high dose antibiotic treatment [58, 59]. Antibiotic diffusion is prevented by a mechanical barrier formed by the extracellular matrix. Further, low oxygen and nutrient concentrations within biofilms create niches with low bacterial metabolic activity. In addtion, up to 1% of bacterial cells in biofilms may be dormant persister cells not affected by antimicrobials . Furthermore, high cell density within biofilms enhances horizontal gene transfer and competition, that together with accumulation of metabolic products, microaerobic areas and oxidative stress, incite DNA damage and provoke the SOS response. Starvation stress in biofilm bacteria was shown to increase the level of tolerance to the fluoroquinolone ofloxacin in
In biofilms, phenotypic variants e.g. small colony variants (SCV), that are slow growing and very tolerant to host defenses and antimicrobials have also been described. SCVs exhibit increased production of exopolysaccharides, can autoaggregate and attach stronly to surfaces [61, 62, 63]. They are potentially responsible for difficult to treat persistent infections, wherein bacteria persist in the host for prolonged periods of time despite antimicrobial therapy. Thus, recalcitrance of biofilms to antimicrobials can be due to tolerance, when dispersed biofilm cells exhibit antibiotic sensitivity and low MIC, as well as resistance, characterized by increased MICs and a resistant phenotype of dispersed biofilm bacteria. The SOS response plays a significant role in biofilm formation but in turn, in the dynamic biofilm environment, SOS inducing factors are generated that promote mutagenesis and diversification.
6. Bacteriocins and phenotypic heterogeneity
Colicins are bacteriocins, toxic proteins that are produced by and act against
Colicins are expressed from strong promoters whose activity is tightly repressed by the LexA protein. Nutrient limitation and DNA damage are major signals that control colicin production [64, 66]. Nevertheless, additional regulators, in conjunction with LexA, have been found to regulate/delay colicin expression. Thus, the global transcriptional factor, IscR, in response to the nutritional status of the cell and, co-dependently with LexA, delays induction of pore-forming colicin genes following SOS induction . On the other hand, temporal induction of DNA and RNA targeting colicins is co-regulated by the AsnC repressor. At the colicin E8,
Colicins have an
Furthermore, monitoring the transcriptional response of
Colicin production has also been found to be a specialized function within a population of genetically identical cells, an example of phenotypic heterogeneity. The colicin K activity gene was shown to be expressed in only a small fraction of a population, while the immunity gene is expressed in the large majority of the cells . A number of colicins are released semispecifically, by cell lysis. Differential expression of the activity and lysis genes prevents excessive lysis. Alternatively, upon DNA damage and induction of the SOS response, all cells express the activity gene. Lysis of the producer releasing colicin as well as lysis of the sensitive target cell, provides material for bacterial shielding or biofilm matrix as well as resources for growth for nonexpressing insensitive cells. A recent study showed ampicillin induced bacterial cell lysis provides a matrix of cell debris that shields viable cells from antimicrobial activity . Further, lysed cells release molecules that could sequester antibiotics.
Subsequently, additional LexA regulated genes, including
Given the mounting threat posed by antibiotic resistance, a better understanding of the mechanisms bacteria employ to evolve resistance, persistence as well as pathogenesis is urgently needed. Conditions conducive to SOS induction are encountered by
This work was funded by grant P1-0198 from the Slovene Research Agency.
Conflict of interest
The authors declare no conflict of interest.