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Chapter 14 : The SOS Responses of Prokaryotes to DNA Damage
Category: Microbial Genetics and Molecular Biology
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The recognition that organisms mount physiological responses to DNA damage initially came from work on Escherichia coli and was surprising to many scientists. This chapter first traces the intellectual development of the present model for SOS regulation in prokaryotes and the identification of genes under SOS control. It considers various molecular mechanisms that are used to fine-tune the expression of individual SOS genes and summarizes our present understanding of the physiology of the SOS responses. The genetic studies of recA, lexA, recA mutants, and lexA mutants indicate the existence of the SOS system. Then, it presents essential elements of SOS transcriptional regulation. It also presents identifying SOS genes by the use of fusions, searching for potential lexA-binding sites and expression microarray analysis. A variety of experiments now support the unifying view that the ultimate signal for SOS induction in vivo is the generation of regions of ssDNA within the cell, which in turn results in the formation of sufficient RecA nucleoprotein filaments to mediate LexA cleavage. Next, the chapter briefly discusses additional subtleties in transcriptional regulation of the SOS responses, and known and putative SOS responses of E. coli from a physiological perspective. Other covered topics are SOS responses in pathogenesis, toxicology, and other bacteria.
Diagrammatic representation of the mechanism by which the lexA-recA regulon is regulated. In the uninduced state (top), LexA repressor protein constitutively expressed in small amounts is bound to the lexA operator and to the operators of the recA gene and other genes under LexA control. These genes are still able to express small amounts of the proteins they encode; thus, there is some RecA protein constitutively present in uninduced cells. Following DNA damage (e.g., the presence of a pyrimidine dimer near a replication fork after induction by UV radiation), the coprotease activity of existing RecA protein is activated, probably by binding to the ssDNA in the gaps created by discontinuous DNA synthesis past the dimers (bottom). The interaction between LexA and activated RecA results in the proteolytic cleavage of LexA. In the induced state (bottom), derepression of the recA+ gene results in the production of large amounts of RecA protein. Other genes under LexA control are also derepressed, although not necessarily with identical kinetics. When the inducing signal disappears (probably by repair of the single-strand gap), the level of active co-protease drops, LexA repressor accumulates, and genes under LexA control are once again repressed. (Adapted from references 163 and 235 .)
When UV-irradiated phage λ is plated on E. coli cells that were previously irradiated, the phage survival is greater than on unirradiated bacteria. This phenomenon was first described by Jean Weigle and is referred to as W (Weigle) reactivation of the phage. (Adapted from reference 427 .)
When wild-type (recA+) cells are UV irradiated and then incubated at either high or low temperatures, the slope of the curve relating mutation frequency to UV dose fits a theoretical two-hit curve. In contrast, recA441 mutants generate mutations at the trp locus with a linear dependency on UV dose; i.e., the slope fits a theoretical one-hit curve. (Adapted from reference 443 .)
lexA(Ind-) mutations are dominant. A lexA2(Ind-) mutant is abnormally sensitive to UV radiation relative to lexA+ or lexA+/lexA+ strains. Following introduction of an episome carrying the lexA+ gene, the UV resistance of the lexA2 strain is not enhanced. The shallower slope of the survival curve at higher UV doses suggests that a small fraction (about 5%) of the lexA2 cells are UV resistant. These may be either lexA+/lexA+ homozygous segregants or haploid lexA+ segregants. (Adapted from reference 286 .)
Extracts of lexA3(Ind-) recA441 cells do not contain high levels of activated RecA coprotease activity, and, so when they are incubated with purified λ repressor in the presence of ATP, no inactivation of repressor (measured by binding to 32P-labeled λ DNA) is observed. However, extracts of mutant lexA(Def) recA441 cells contain high levels of activated coprotease, and these extracts degrade λ repressor in vitro. (Adapted from reference 337 .)
Cleavage of λ repressor protein in vitro has a requirement for RecA protein, ssDNA, and ATP or ATPγ-S. Following gel electrophoresis of incubation mixtures, RecA protein, λ repressor, and degraded λ repressor can be observed in the appropriate lanes. (Adapted from reference 66 .)
Induction of protein X (RecA). Nalidixic acid was added at a final concentration of 35 μg/ml to cultures of E. coli lexA+ and lexA(Ind-) strains. At various times after the addition of nalidixic acid, samples were removed and pulsed with [35S] methionine for 8 min. Membrane proteins were prepared, separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and autoradiographed. Lanes: a, lexA+, no nalidixic acid; b to d, lexA+ 10, 40, and 70 min, respectively, after nalidixic acid addition; e, lexA (Ind-), no nalidixic acid; f to h, lexA (Ind-) 10, 40, and 70 min, respectively, after nalidixic acid addition. A portion of the autoradiograph is depicted. (Adapted from reference 140 .)
(A) Operator regions near the beginning of representative SOS-regulated genes have similar base sequences, about 20 bp long, that are binding sites for the LexA repressor. The binding sites for LexA are often referred to as “LexA boxes” or “SOS boxes.” The lexA+ gene has two nearly identical SOS boxes. (B) Operator-constitutive (Oc) mutations in representative SOS genes. Boxed nucleotides are the most highly conserved nucleotides in the consensus recognition sequence ( 430 ) of the LexA repressor (LexA box). The letters shaded in gold indicate single-base-pair mutations that are Oc mutations. Oc mutations have been detected and characterized in the context of mucA+B+, recA+, lexA+, and umuD+C+ operators. (Panel A adapted from references 107 and 163 and supplemented with sequences from reference 65 ; panel B adapted from references 363 and 384 .)
LexA fragments generated by autocleavage at its A84-G85 bond are degraded by ClpXP. The SOS response was induced with nalidixic acid, protein synthesis was blocked with chlorampenicol, and the half-lives of intact LexA and the two cleavage fragments were monitored by Western blotting in clpX+ and clpX - cells. LexA, LexA1-84, and LexA85-202 were identified by comparison with autocleaved LexA (lane S). (Adapted from reference 293 .)
Proposed mechanism for LexA repressor cleavage. (Adapted from reference 377 .)
Sequence alignment of the C-terminal domains of members of the LexA superfamily. Sequences of the C-terminal domains of E. coli LexA and B. subtilis (B. subt) LexA (DinR), UmuD, MucA, and the repressors of bacteriophages X and 434 (P. Lambda and P. 434 , respectively) were aligned by Clustal W ( 402 ). Headings give the name of the protein, the organism name in parentheses, and the number of the starting sequence residue. Sequences, residue numbers, and β strands of E. coli LexA repressor, UmuD’, and λcI repressor, respectively, are color coded in various shades of gold. The C-terminal domains contain a cleavage site region, a structurally conserved catalytic core, and an intervening linker loop that has been proposed to be involved in domain swapping and intermolecular cleavage in this family of autoproteinases. The cleavage site region in LexA has a strand-loop-strand topology (b3-loop-b4). A segment of the LexA cleavage site region assumes a variable conformation (residues Val79 to Glu95). The positions for RecAspecific mutants of λcI, hypercleavable Inds mutants of LexA, and noncleavable Ind- mutants of LexA are marked by squares, circles, and triangles, respectively. (Adapted from reference 252 .)
Two conformational states of LexA. (Left) Ribbon diagram of the C-terminal domain of the LexA Δ 1-67 S119A mutant with the cleavage site region in the noncleaving form. The cleavage site region is colored in gold, and the Ala84-Gly85 cleavage site lies far from the oxyanion hole (circled), where proteolytic cleavage occurs. (Right) In the cleavage-active form, the cleavage site region moves almost 20 Å to position the Ala84-Gly85 cleavage site in the oxyanion hole containing the active-site residues Ser119 and Lys56 (see Fig. 14–13 ). (Adapted from reference 252 .)
Surface representation showing the active site of LexA. In the active conformation, the Ala84-Gly85 cleavage substrate binds in a pocket resembling the oxyanion hole of other proteases. The side chains of Lys156 and Ser119 are positioned to assist peptide cleavage (see Fig. 14–12 ). (Adapted from reference 252 .)
Three-dimensional model of the RecA-DNA filament. A three-dimensional reconstruction of RecA bound to dsDNA based on electron microscopy shows a distinctive repeating shape corresponding to individual RecA subunits within the filament (grey surface) ( 409 ). The pitch of the RecA filament bound to DNA is different from that of RecA (gold ribbon) that was crystallized in the absence of DNA, and a rotation of the RecA subunits is required to dock the crystal structure into the electron microscopy reconstruction of the filament. (Image courtesy of Edward H. Egelman.)
(A) Creation of an operon fusion to lacZ by the insertion of Mu d1 into a chromosomal gene. In such a fusion, the expression of β-galactosidase is now regulated by the control region of the chromosomal gene. (B) Kinetics of induction of β-galactosidase in strains carrying lacZ fusions to SOS genes. Mitomycin C (MC) at 1 μg/ml was added to exponentially growing cultures as indicated. Aliquots were removed periodically, and the total activity of β-galactosidase present in the culture was determined. Cell density was determined by measuring the absorbance at 600 nm (A600). For panels a to d: gold line, untreated fusions; black line, fusion strains plus mitomycin C; gold line, lexA(Ind-) fusion strains plus mitomycin; gold line, recA(Def) derivatives plus mitomycin. For panel a only: gold line, X::Mu d1/pKB280 (pKB280 is a plasmid that overproduces λ repressor). Ap, ampicillin resistance; A, Y, and Z, lacA, lacY, and lacZ, respectively. (Adapted from references 183 and 421 .)
Transcriptional induction following UV irradiation in the genes surrounding known LexA boxes measured using DNA microarrays. The change in transcript levels for the indicated gene is plotted over time. The arrows indicate the direction of transcription within the operon relative to the LexA box. Arrows pointing left are transcribed on the minus strand, and arrows pointing right are transcribed on the plus strand. The locations and distances, in base pairs, of the LexA box from the initial ATG codon are indicated in the boxes. The graphs of genes that are directly adjacent on the chromosome are joined. The location of the gene(s) on the chromosome, in kilobase pairs, is indicated along the top of each plot. Solid black, irradiated wild type; dotted black, unirradiated wild type; solid gold, irradiated lexA1 (Ind-); dotted gold, unirradiated lexA1 (Ind-). Time points in which the PCR or hybridization failed, or the fluorescent signal generated by the unirradiated sample was <30% above the background level of fluorescence, are not plotted. ysdAB, dinQ, and dinS were not examined. (Adapted from reference 65 .)
Model for how the transducing signal generated by a dsDNA break leads to SOS induction. (A) DNA damage produces a dsDNA break. (B) RecBCD enzyme processes the broken DNA, degrading 3’ → 5’ until a χ site is recognized, at which time RecBCD enzyme pauses, the exonuclease activity is attenuated, and RecA protein is loaded onto the χ-containing DNA strand within an ssDNA loop. (C) The nuclease polarity is then switched, with continued degradation occurring 5’ → 3’, leading to the production of a 3’ ssDNA overhang that is coated with RecA protein. (D) The RecA-ssDNA nucleoprotein filament that is assembled on the χ-containing ssDNA stimulates the autocleavage of the LexA repressor. (E) Once LexA is cleaved, it is no longer able to bind to the operators (OP) of SOS-regulated genes, thereby leading to their transcription. The arrow indicates that χ has a directionality. (Adapted from reference 5 .)
Inhibition of initiation of DNA replication blocks UV-induced LexA cleavage. dnaC(Ts) uvrB (A) or wild-type (B) cells were grown at 32°C. When the cell density of the cultures reached 108 cells per ml, the cells were diluted twofold with medium prewarmed to 55°C to establish a temperature of 42°C instantly. At 70 min after the temperature shift, the cells were UV irradiated with a dose of 5 J/m2 and the rate of LexA decrease at 42°C (gold line) was compared with that obtained with control cells kept at 32°C (black line). (Adapted from reference 357 .)
Decrease in LexA concentration following irradiation with UV. Exponentially growing wild-type (w.t.) and uvrA cells were UV irradiated (time zero) at 37°C for 20 s at 5 J/m2 in the absence or presence of 60 μg of chloramphenicol (Cam) per ml added 90 s before irradiation with UV. As a control, chloram-phenicol was added to unirradiated cells. At the indicated times, cells were analyzed for their LexA content by immunoblotting. (A) Quantification of LexA by densitometry. Gold solid line, wild-type cells plus UV; black line, wild-type cells plus chloramphenicol; gold dotted line, uvrA cells plus UV; grey line, wild-type cells plus UV plus chloramphenicol. (B) Semilogarithmic plot of the disappearance of LexA in chloramphenicol-treated wild-type cells (same data as in panel A). Black line, wild-type cells plus chloramphenicol; gold line, wild-type cells plus UV plus chloramphenicol. The inset shows the LexA disappearance over the first 3 min after irradiation of wild-type cells with UV. (Adapted from reference 357 .)
Disposition of the different SOS operators (black boxes) with respect to the promoters of the SOS genes. The promoters are characterized by their —35 regions (consensus sequence, TTGACA) and their —10 regions (consensus sequence, TATAAT). The corresponding regions are shown as gold boxes if at least four base pairs are identical to the consensus sequence; otherwise, these regions are shown as open boxes. The identification of these promoter motifs is reliable for genes whose transcriptional start site has been mapped but is tentative for polB+ and ruvA+B+. Black dots over some bases of the 5 ‘ ends of the mRNA represent alternative transcription start sites. (Adapted from reference 363 .)
A negatively charged surface of DinI may function as a DNA mimic. A series of acidic amino acids (gold) decorate the surface of the DinI C-terminal α-helix ( 412 ). This patch of negative charge may mimic the charged backbone of DNA and compete with DNA for binding to RecA. The proposed mimicry of DNA by the inhibitory DinI protein is similar to that observed for UGI, a protein inhibitor of uracil DNA glycosylase that interacts with the DNA-binding surface of the enzyme (see Chapters 6).
Three-dimensional reconstruction of RecA-DNA-RecX filaments. The additional density due to RecX is displayed in grey, while the surface of a reconstruction of RecA alone is shown in gold. (Adapted from reference 407 .)
Evidence that SOS induction increases the efficiency of global repair of UV-induced CPD but not of pyrimidine-pyrimidone (6–4) photoproducts [(6–4)PP]. (A and B) Rifampin inhibits global repair of CPDs but not (6–4)PP. Monoclonal antibodies specific for CPDs (A) and (6–4)PP (B) were used in an immunoassay with DNA isolated at the indicated times after UV irradiation at 40 J/m2. (C and D) Constitutive expression of the SOS response results in rapid repair of CPDs and (6–4)PP and eliminates rifampin inhibition of genomic CPD repair. Monoclonal antibodies specific for CPDs (C) and (6–4)PP (D) were used in an immunoassay with DNA isolated from lexA51 (Def) cells at the indicated times after UV irradiation at 40 J/m2. Black lines indicate untreated cells; gold lines indicate cells treated with 50 μg of rifampin per ml. (E and F) Constitutive expression of the SOS response leads to rapid repair of CPDs in both strands of the lactose operon regardless of rifampin treatment. Transcription-coupled repair assays were performed on DNA isolated from lexA51 (Def) cells left untreated (E) or treated with 50 μg of rifampin (RIF) per ml (F). Dotted black lines indicated transcribed strand (TS); dotted gold lines indicate nontranscribed strand (NTS). (Adapted from reference 68 .)
Evidence that treatment of cells with SOS-inducing agents results in a fast and massive intracellular coaggregation of RecA and DNA into a lateral macroscopic assembly. (A to D) Electron microscopy of wild-type E. coli cells exposed to DNA-damaging agents. (A) Wild-type E. coli cells at mid-logarithmic phase. The dark particles are ribosomes. The ribosome-free spaces contain chromatin. (B) Wild-type cells treated with nalidixic acid for 30 min. A similar morphology is exhibited by UV-irradiated bacteria. (C) Cells treated with nalidixic acid in the presence of spermidine (2.5 mM) for 2 h. (D) High magnification of the assembly shown in panel C. Identical morphologies are detected in bacteria fixed by either cryofixation or chemical methods. Because these two fixation modes proceed through fundamentally different mechanisms, detection of the assemblies in the two procedures is consistent with these structures representing a genuine morphological feature. (Scale bars are 200 nm in panels A, B, and D and 500 nm in panel C.) (E to H) In situ localization of DNA and RecA. (.E) Cells at mid-logarithmic phase, stained solely with the DNA-specific reagent osmium-ammine-SO2. The irregular spreading of chromatin over the cytoplasm is indicated. (F and G) Identical staining to that in panel E, but after treatment of bacteria with nalidixic acid for 60 min. (H) Immunogold labeling of E. coli cells exposed to nalidixic acid for 60 min, by using anti-RecA antibodies and gold-conjugated immunoglobulin G (detected as electron-dense dots). Exclusive localization of RecA within the ordered assembly (highlighted by an arrow) is noted. (Adapted from reference 218 with permission.)
Fluorescence microscopy images of live uvrA+-gfp B. subtilis cells. The uvrA gene is expressed from its native chromosomal promoter, and the fusion to GFP does not interfere with the function of UvrA. Cultures growing exponentially were split equally, and half was UV irradiated or treated with mitomycin C depending on the experiment. The parallel cultures were allowed to continue growing for 1 h. Aliquots of live cells were then stained with 4’6-diamidino-2-phenylindole and a vital membrane dye and then viewed under the microscope. (A) Exponentially growing uvrA-gfp+ cells. (B) uvrA-gfp+ cells 1 h after UV irradiation at 25 J/m2. (C) uvrA-gfp+ cells 1 h after treatment with mitomycin C (0.25 μg/ml). (Adapted from reference 379 .)
Inhibition of FtsZ polymerization by SulA. The crystal structure of FtsZ complexed to SulA ( 63 ) shows how the SulA dimer binds two subunits of FtsZ and thereby blocks the formation of a ring by FtsZ. SulA binds to the subunit interface of FtsZ that would otherwise contact the GDP-binding surface of FtsZ in the ring-shaped polymer.