Genes regulated by the Escherichia coli SOS repressor LexA exhibit heterogenous expression
© Kamenšek et al; licensee BioMed Central Ltd. 2010
Received: 16 July 2010
Accepted: 11 November 2010
Published: 11 November 2010
Phenotypic heterogeneity may ensure that a small fraction of a population survives environmental perturbations or may result in lysis in a subpopulation, to increase the survival of siblings. Genes involved in DNA repair and population dynamics play key roles in rapid responses to environmental conditions. In Escherichia coli the transcriptional repressor LexA controls a coordinated cellular response to DNA damage designated the SOS response. Expression of LexA regulated genes, e.g. colicin encoding genes, recA, lexA and umuDC, was examined utilizing transcription fusions with the promoterless gfp at the single cell level.
The investigated LexA regulated genes exhibited heterogeneity, as only in a small fraction of the population more intense fluorescence was observed. Unlike recA and lexA, the pore forming and nuclease colicin activity genes as well as umuDC, exhibited no basal level activity. However, in a lexA defective strain high level expression of the gene fusions was observed in the large majority of the cells. All of the investigated genes were expressed in a recA defective strain, albeit at lower levels, revealing expression in the absence of a spontaneous SOS response. In addition, the simultaneous expression of cka, encoding the pore forming colicin K, and lexA, investigated at the single cell level revealed high level expression of only cka in rare individual cells.
LexA regulated genes exhibit phenotypic heterogeneity as high level expression is observed in only a small subpopulation of cells. Heterogenous expression is established primarily by stochastic factors and the binding affinity of LexA to SOS boxes.
Genetically identical bacterial cells can exhibit heterogeneity as the population bifurcates into distinct subpopulations. Such heterogeneity within clonal populations is a bet hedging strategy as a small fraction of a population is either prepared to survive adverse environmental conditions or sacrifice itself to enhance the likelihood of survival of clonal siblings. Examples of phenotypic heterogeneity include: development of competence and sporulation in Bacillus subtilis, lysogenic versus the lytic cycle of bacteriophage lambda, biofilm formation, toxin production and antibiotic persistence [1–4].
In Escherichia coli DNA damage induces the expression of more than 40 genes leading to arrest of cell division and the induction of DNA repair, prophages, toxin production and mutagenesis . The key regulator of this coordinated cellular response, named the SOS response , is the LexA protein that represses gene expression by binding as a dimer to a 16-mer consensus sequence CTG-N10-CAG designated as SOS boxes . Upon DNA damage replication forks are stalled exposing single-stranded DNA (ssDNA). RecA binds to the ssDNA forming a nucleoprotein filament which activates the autoproteolytic cleavage of LexA, leading to induction of the SOS response. In addition to activation by exogenous DNA damaging agents, the SOS response is also induced by endogenous, as well as spontaneous events .
SOS induction often results in the production of antimicrobial toxins such as bacteriocins. The bacteriocins of E. coli strains, designated as colicins, are plasmid encoded and are found with high frequency among natural isolates . These toxins were suggested to promote phenotypic and genotypic diversity within E. coli populations in the mammalian colon [9, 10]. Colicins destroy cells by one of three mechanisms: (i) they either form pores in the cytoplasmic membrane thus depleting its electrochemical potential, (ii) degrade either the DNA or RNA of their target cell or (iii) inhibit peptidoglycan and lipopolysaccharide (LPS) O-antigen biosynthesis [11–13]. Production and release of most colicins is encoded by three genes, an activity gene encoding the colicin protein, an immunity gene encoding a protein that protects the cell from its produced toxin and a lysis gene for semispecific release of the colicin. Colicin encoding genes characteristically have two overlapping SOS boxes that bind two LexA dimers and protect the cell from untimely colicin production, as it is lethal to the producing cell . Some colicins, such as colicins B and M, have no lysis genes and are actively secreted by an unknown mechanism . Colicin B and M encoding operons are tightly linked on large conjugative plasmids [16, 17]. Expression of both colicin B and colicin M seems to be regulated by a common SOS boxes located upstream of the colicin B activity gene [16, 18].
In previous studies we showed that the pore forming colicin K activity gene cka is expressed in only a small fraction of a bacterial population while the immunity gene encoding the immunity protein is expressed in the large majority of the cells [3, 19]. In the present study we investigated, at the single cell level, expression of the activity genes of several other colicins namely, the pore formers A, E1 and N, the DNase colicin E7 and the LPS synthesis inhibitor, colicin M. We compared the single cell colicin expression to the expression of other LexA regulated genes, e.g. recA, lexA and umuDC, and finally we examined the simultaneous expression of the colicin encoding cka gene and the lexA gene.
Bacterial strains, plasmids and growth conditions
E. coli strains and plasmids used in the presented study
thr-1 araD139 Δ(gpt-proA)62 lacY1 tsx-33 supE44 galK2 hisG4 rpsL31 xyl-5 mtl-1 argE thi-1 sulA211
RW118 lexA51 (Def)
pSC101 low copy plasmid origin with promoterless GFPmut3 gene, Knr
caa cai cal
A. P. Pugsley
cna cni cnl
A. P. Pugsley
ce1a ce1i ce1l
A. P. Pugsley
ce7a ce7i ce7l
A. P. Pugsley
A. P. Pugsley
DsRed-Expre ss2 reporter Knr
cka-gfp Apr Knr
General DNA techniques
Plasmid DNA isolation was performed with the GeneJET™ plasmid miniprep kit (Fermentas, Burlington, Canada). Standard procedures were used for gel electrophoresis, ligations and transformation experiments . Restriction endonuclease digestion was performed according to the instructions of the manufacturer (Fermentas). The PCR amplified fragments were purified using the QIAquick PCR purification kit (Qiagen, Hamburg, Germany). DNA fragments were isolated from agarose gels by using a QIAquick gel extraction kit (Qiagen).
Construction of promoter fusions
Primers used in this study
nucleotide sequence 5'-3'
The promoterless DsRed-Express2 gene, which is part of a gene cassette on plasmid pDsRed-Express2-N1, was cloned into the natural colicin K encoding plasmid pColK-K235 manipulated to carry the Apr gene as a selectable marker, and a Kpn I restriction site in the cka gene. A cassette carrying the promoterless gfp was inserted at the KpnI restriction site . The cka-DsRed-Express2 transcriptional fusion was constructed by replacing the Kpn I fragment harboring the promoterless gfp with the in frame promoterless DsRed-Express2 amplified by PCR (Table 2) which was prior to ligation also cut with Kpn I. Only cells with an active cka promoter can express DsRed-Express2.
Nucleotide sequencing was performed to confirm that no base changes had occurred during amplification. The sequences have been deposited in the GenBank Nucleotide sequence database under accession numbers, HM449002 (caa promoter region), HM449003 (cna promoter region), HM449004 (ce1a promoter region), HM449005 (ce7a promoter region), HM449006 (cma promoter region).
Strains RW118 and RW464 carrying different colicin promoter region-gfp transcriptional fusions, and control strains without plasmid carrying gfp fusions, were grown with aeration at 37°C. Samples were removed at early stationary phase and chloramphenicol (500 μg ml-1) (Sigma) was added to block protein synthesis. Prior to microscopy, cells were attached to glass slides coated with 0.1% (wt vol-1) poly-L-lysine (Sigma). Fluorescence microscopy to detect expression in single cells was performed using an inverted microscope (Nikon Eclipse TE300), equipped with a Nikon digital camera DXM 1200, and a 488 nm Argon-Ion laser as well as bright field microscopy.
The examined cells were counted with software for quantification of bacteria by automated image analysis cellC http://www.cs.tut.fi/sgn/csb/cellc/. The fluorescence intensity of individual cells was estimated using image analysis software Scion Image http://www.scioncorp.com as previously described . The fluorescent micrographs were converted to greyscale images. The density window was established by using density slice matching the shape of the cells with the highest fluorescence intensity and that of the cells with the lowest intensity, gaining the top and the bottom boundaries (respectively) of the density window. For greater clearness the density index scale is determined from 0 (black) to 256 (white). All micrographs were taken at exactly the same conditions; thus the density window gives good correlation to the fluorescence intensity of the analyzed population.
Simultaneous expression of the cka-DsRed-Express2 and the lexA-gfp fusions was investigated employing a laser scanning Confocal Microscope (Zeiss, Göttingen, Germany).
Results and discussion
Pore forming and nuclease colicins exhibit heterogeneity
Cells expressing SOS regulated genes in the wild type RW118
gfp transcriptional fusion
% of intensely fluorescent cells
Fluorescence threshold level*
SOS genes exhibit heterogeneity
Previously, single cell expression of a sulA-gfp fusion was investigated . SulA is synthesized in large amounts during the SOS response and inhibits cell division by binding to FtsZ, the major component of the cell division machinery . The sulA operator has a HI of 4.65 and thus binds LexA tightly. The authors found that in the absence of exogenous DNA damaging agents only approximately 0.3% of the examined cells fully expressed sulA.
The SOS genes, polB, dinB and umuDC, encode specialized DNA polymerases II, IV and V respectively, which can bypass DNA lesions yet with reduced fidelity introducing mutations to newly synthesized DNA . The operon encoding PolV is regulated by an SOS box that exhibits one of the highest predicted LexA binding affinities, with a HI of 2.77 . It was shown that only upon full induction of the SOS response UmuD is synthesized and persists as a full length dimer . Accordingly, fluorescence emission from the umuDC-gfp fusion was observed in a very small fraction of the examined cells (0.09%) and no detectable basal level of expression was observed among the large majority of the population. Our results show that in the absence of exogenous DNA damaging agents very low levels of umuDC promoter activity is detected. As translesion synthesis must be employed only when necessary, synthesis of the specialized polymerases is under physiological conditions controlled by complex regulation at the level of transcription and posttranslation.
SOS regulated genes are expressed in a recA defective strain
Cells expressing SOS regulated genes in the recA defective strain RW464
gfp transcriptional fusion
% of intensely fluorescent cells
Fluorescence threshold level*
Both the recA-gfp and lexA-gfp fusions were expressed in the recA defective strain RW464, albeit at a lower level compared to the wild type (Table 4, Figure 2, Figure 3), with a small fraction of the population exhibiting high fluorescence indicating that, stochastic factors could be involved. Filamentation due to delay in cell division is evident among the less robust recA defective strain. However, expression of the investigated genes was not limited to filamented cells (Figure 3).
To resolve the effect of LexA regulation at the single cell level, expression of the investigated gene fusions was also studied in strain RW542 encoding a LexA protein defective in binding to LexA boxes. Fluorescence microscopy revealed that in the lexA defective strain all cells harboring the lexA-gfp or recA-gfp fusions, as well as the large majority (98%) of the cells harboring gfp fusions with the colicin activity genes were intensely fluorescent, indicating high level expression (data not shown).
Simultaneous expression of the cka and SOS genes
In conclusion, to our knowledge this is the first study exploring a number of SOS regulated genes at the single cell level under physiological condition. Exposure of a population of bacterial cells to a DNA damaging agent induces the SOS response in all susceptible cells. However, under physiological conditions, genes regulated by the LexA protein also exhibit heterogenous expression. We show that genes with a very high affinity of LexA binding, characteristic of overlapping SOS boxes of colicin operators, or very low HI such as umuDC, are expressed in only a small fraction of the population and exhibit no detectable basal level expression. In contrast, genes of the SOS regulon with a somewhat lower predicted affinity of LexA binding, such as lexA and recA, while also fully expressed in a small subpopulation, exhibit basal level expression. Intense fluorescence of cells harboring the investigated gene fusions was observed in a lexA defective strain indicating that the LexA protein effectively represses promoter activity in the large majority of cells. Some of the examined cells could be experiencing disruption of replication forks during replication and thus induction of the SOS response. However, expression of all of the investigated genes was observed in a recA mutant, which cannot instigate an SOS response indicating that, expression of LexA regulated genes also occurs stochastically.
Expression of colicin genes under physiological conditions by a small subpopulation may promote strain and genetic diversity and due to lysis of producing cells could provide resources to facilitate growth of non-expressing cells. On the other hand, a subpopulation of cells with higher levels of the RecA protein may be more proficient in recombination, e.g. for the stable incorporation of horizontally acquired DNA or a rapid response to DNA damage. We can speculate that heterogeneity of expression of lexA in E. coli affects a number of phenomenon significant for antibiotic tolerance/resistance (persisters), horizontal gene transfer (induction of prophage) and virulence among pathogenic E. coli strains. The same might apply to other gram negative (e.g. Shigella, Salmonella, Pseudomonas aeruginosa) and gram positive (e.g. S. aureus, B. subtilis) bacterial species that possess a system similar to the E. coli SOS system.
LexA regulated SOS genes exhibit heterogeneity as they are highly expressed in only a small subpopulation of cells. Unlike recA and lexA, the colicin activity genes and umuDC exhibit no basal level expression. Heterogenous expression is established primarily by stochastic factors as well as the binding affinity of LexA to SOS boxes.
We thank Ben Glick for generously providing pDsRed-Express2-N1 as well as Uri Alon for strains carrying the lexA-gfp, recA-gfp and umuDC-gfp fusions. This work was funded by grant P1-0198 from the Slovenian Research Agency (ARRS) and the FP6 Sixth EU framework programme for Research and Technological Development: Transnational Access, Dryland Research Specific Support Action (SSA), Jacob Blaustein Institutes of Desert Research, Ben Gurion University of the Negev.
Simona Kamenšek is a recipient of a Ph.D grant from ARRS.
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