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Copyright 2001 by the Genetics Society of America
Comparative Gene Expression Profiles Following UV Exposure in Wild-Typeand SOS-Deficient Escherichia coli
Justin Courcelle,*,1 Arkady Khodursky,†,1 Brian Peter,‡ Patrick O. Brown† and Philip C. Hanawalt§
†Department of Biochemistry, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, ‡Department of MCB,UC-Berkeley, Berkeley, California 94720, *Department of Biological Science, Mississippi State University, Mississippi State,
Mississippi 39762 and §Department of Biological Sciences, Stanford University, Stanford, California 94305
Manuscript received October 4, 2000Accepted for publication January 29, 2001
ABSTRACTThe SOS response in UV-irradiated Escherichia coli includes the upregulation of several dozen genes
that are negatively regulated by the LexA repressor. Using DNA microarrays containing amplified DNAfragments from 95.5% of all open reading frames identified on the E. coli chromosome, we have examinedthe changes in gene expression following UV exposure in both wild-type cells and lexA1 mutants, whichare unable to induce genes under LexA control. We report here the time courses of expression of thegenes surrounding the 26 documented lexA-regulated regions on the E. coli chromosome. We observed17 additional sites that responded in a lexA-dependent manner and a large number of genes that wereupregulated in a lexA-independent manner although upregulation in this manner was generally notmore than twofold. In addition, several transcripts were either downregulated or degraded following UVirradiation. These newly identified UV-responsive genes are discussed with respect to their possible rolesin cellular recovery following exposure to UV irradiation.
IRRADIATION of growing Escherichia coli cultures the genes normally suppressed by LexA are more fre-quently transcribed (Sassanfar and Roberts 1990 andwith ultraviolet light (UV) produces DNA lesions
that at least transiently block the essential processes of references therein; Friedberg et al. 1995). An interest-ing feature of the LexA/RecA regulatory circuit is thatreplication and transcription. A large amount of work
has demonstrated that the cell responds to this stress the timing, duration, and level of induction can varyfor each LexA-regulated gene, depending upon the lo-by upregulating the expression of several genes thatcation and binding affinity of the LexA box(es) relativefunction to repair the DNA lesions, restore replication,to the strength of the promoter. As a result of theseand prevent premature cell division. A number of otherproperties, some genes may be partially induced in re-genes are known to be upregulated, yet remain function-sponse to even endogenous levels of DNA damage, whileally uncharacterized. The changes in gene expressionother genes appear to be induced only when high orin response to DNA damage produced by UV and somepersistent DNA damage is present in the cell. In fact,other environmental agents have been collectively ter-the SOS response may represent a continuum in themed the SOS response, after the international distressmonitoring of environmental stress, rather than simplysignal (Radman 1974 and reviewed in Friedberg et al.operating as an emergency switch following acute injury.1995; Koch and Woodgate 1998).
The first systematic search for damage-inducible (din)Many of the DNA damage-induced genes are nega-genes was carried out by Kenyon and Walker (1980)tively regulated by the LexA repressor protein, whichby randomly inserting a lac reporter gene into the E.binds to a 20-bp consensus sequence in the operatorcoli chromosome to identify promoters that were upreg-region of the genes, suppressing their expression (Brentulated following DNA damage in a recA/lexA-dependentand Ptashne 1981; Little et al. 1981). Derepressionfashion. Using this same technique, subsequent studiesof these genes occurs when the RecA protein binds toidentified additional din genes and in some cases identi-single-stranded regions of DNA created at replicationfied genes previously characterized to be involved in theforks when they are blocked by DNA damage. RecArecovery from DNA damage (Bagg et al. 1981; Foglianobound to single-strand DNA becomes conformationallyand Schendel 1981; Huisman and D’Ari 1981; Kenyonactive, serving as a coprotease to cleave the LexA repres-and Walker 1981; Shurvinton and Lloyd 1982;sor. As the cellular concentration of LexA diminishes,Lloyd et al. 1983; Siegel 1983; Bonner et al. 1990;Iwasaki et al. 1990; Ohmori et al. 1995b). Analysis ofthe known din genes revealed a 20-bp consensus LexA-
Corresponding author: Justin Courcelle, Department of Biological binding motif, or “SOS box,” shared by these genesScience, P.O. Box GY, Mississippi State University, Mississippi State,in their promoter/operator regions (Walker 1984),MS 39762. E-mail: [email protected]
1 These authors contributed equally to this work. which has been used in more recent studies to systemati-
Genetics 158: 41–64 (May 2001)
42 J. Courcelle et al.
from a fresh overnight culture into 200 ml Davis media andcally search and identify additional lexA-regulated genesincubated in a 1-liter Erlenmeyer flask at 378 in a New Bruns-(Lewis et al. 1994; Ohmori et al. 1995a; Fernandez Dewick Scientific (Edison, NJ) model G76 gyrotory water bath
Henestrosa et al. 2000). These studies in total have at 220 rpm to midlog (OD600 0.4, z2 3 108 cells/ml). A 15-Widentified 31 genes under lexA/recA control. germicidal lamp (254 nm, 0.66 J/m2/sec at the sample posi-
tion) provided the UV irradiation. A total of 70 ml of cultureOther genes have been reported to be upregulatedwas placed into a 15-cm-diameter glass petri dish and irradi-following DNA damage but are believed to be indepen-ated for 60 sec with gentle agitation. Two 65-ml unirradiateddent of the lexA regulon. In some cases, the inductionsamples were also agitated in a 15-cm petri dish but were not
is thought to be dependent on recA, but independent exposed to UV. A total of 70 ml of irradiated culture (in afrom the LexA repressor. In other cases, genes have 500-ml Erlenmeyer flask) and 30 ml of unirradiated culture
(in a 250-ml Erlenmeyer flask) were then returned to thebeen shown to be upregulated independently from bothshaking water bath for the duration of the time course. AtrecA and lexA (Friedberg et al. 1995; Koch and Wood-the appropriate times, 10-ml samples were placed into 20 mlgate 1998). The mechanism of regulation in these casesof ice-cold NET (100 mm NaCl, 10 mm Tris, 10 mm EDTA),
is not understood. An additional, although as yet unex- pelleted by centrifugation, washed with 1 ml cold NET, re-plored, possibility is that some genes may be repressed pelleted, and frozen at 2808. The limited availability of mi-
croarray chips constrained this experiment to a single timeor their transcripts may be degraded in response tocourse containing seven samples (five irradiated, two unirradi-DNA damage.ated) for each strain.It was of interest to us not only to learn whether
Microarray procedures: Relative mRNA levels were deter-additional genes can be regulated in a LexA-dependent mined by parallel two-color hybridization to cDNA microarraysmanner but also to determine whether other cellular representing 4101 open reading frames (ORFs) representing
95.5% of E. coli ORFs according to Blattner et al. (1997).responses to UV irradiation exist that are lexA indepen-cDNA arrays were manufactured as described in MGuide atdent. The lexA1 allele encodes an amino acid changehttp://cmgm.stanford.edu/pbrown/mguide/index.html. To-at a position that is essential for the cleavage and inacti-tal mRNA was extracted from 2–5 3 109 cells using QIAGEN
vation of LexA (Slilaty and Little 1987). Thus, in (Chatsworth, CA) RNeasy spin columns. A total of 25–30 mglexA1 mutants, the LexA1 concentration remains high of total RNA was labeled with Cy-3-dUTP (or Cy-5-dUTP) inand LexA-regulated genes are not induced, even in the a standard reverse transcriptase (RT) reaction by Superscript
II (1) (GIBCO BRL, Gaithersburg, MD) with 1 mg of randompresence of high levels of activated RecA. Thereforehexamer (Pharmacia, Piscataway, NJ) primers. Following puri-this system should allow an analysis of gene expressionfication through Microcon-30 (Millipore, Bedford, MA)that occurs independent of the LexA repressor. (MGuide), Cy-3- and Cy-5-labeled cDNA were combined with
The changes in gene expression in the entire genome SSC (2.53 final), SDS (0.25%), and 40 mg of E. coli rRNAcan be measured simultaneously using high-density (Boehringer Mannheim, Indianapolis) in a final volume of
16 ml and hybridized to a DNA microarray for 5 hr at 658.cDNA microarrays (Schena et al. 1995). DNA microar-Slides were washed as described in MGuide and scanned usingrays contain PCR-amplified DNA fragments of knownan AxonScanner (Axon Instruments, Foster City, CA; GenPixand predicted genetic sequences that are printed on 1.0) at 10 mm per pixel resolution. Acquired 16-bit TIFF im-
the surface of a glass slide. Through the comparative ages were analyzed using ScanAlyze software, which is publiclyhybridization of two cellular RNA preparations, the rela- available at http://rana.stanford.edu/software/.
Comparative measurements of transcript abundance: Timetive difference between transcript levels of any genecourse samples were analyzed directly by comparing the abun-in these preparations can be determined. Using thedance of each gene’s transcripts relative to the t0 sample. RNAcomplete sequence of the E. coli genome (Blattner etsamples taken during the time course were labeled with Cy-5,
al. 1997), DNA microarrays were prepared containing and RNA from the t0 sample was labeled with Cy-3.PCR products corresponding to 95.5% (4101 out of Sequence analysis: Nucleotide sequences in the regions of4295) of all annotated open reading frames in the E. induced genes were examined using the COLIBRI program
provided by the Pasteur Institute at http://genolist.pasteur.fr/coli genome (Khodursky et al. 2000). We utilized thesecolibri/. Regions surrounding induced genes were searchedmicroarrays to follow the changes in gene expressionfor the consensus sequence CTG(N)10CAG, allowing for oneoccurring during the first hour following UV irradiation mismatch. Matching sequences that fell between 2400 and
in the wild-type strain, MG1655, and in an isogenic lexA1 1100 bp of a start codon were then examined for their heterol-mutant. ogy index. The heterology index was determined as reported
in Lewis et al. (1994) on the basis of the formula developedby Berg and von Hipple (1988). Heterology index 5o ln[(n(consensus) 1 0.5)/(n(actual) 1 0.5)], where n(consensus)MATERIALS AND METHODSrefers to the number of times that the most common, orconsensus, base occurs at a given position in the set of knownBacteria: Strain MG1655 was used as the wild-type strainbinding sites, and n(actual) refers to the number of times thatin this study since its genome has been completely sequencedthe base being analyzed occurs at the same position in the(Blattner et al. 1997). The MG1655 lexA1(Ind2) malB::Tn9set of known binding sites. n values for each position of thewas constructed by P1-mediated transduction of the lexA1 al-20-bp LexA binding site were determined using the knownlele from strain GC2281 (Taddei et al. 1995) into strainLexA-binding sites shown in Figure 1A and their respectiveMG1655. Transfer of the lexA1 allele was verified by resistancecomplementary sequences.to chloramphenicol and hypersensitivity to UV irradiation.
Nomenclature: All genes are named according to the RuddGrowth and irradiation: Cells were grown in Davis mediumplus 0.4% glucose. Cultures were inoculated at a 1:200 dilution system at http://bmb.med.miami.edu/ecogene/ecoweb (Rudd
43E. coli Gene Expression Profiles After UV
2000). In cases where we found no corresponding Rudd gene plotted in Figure 2A. For most of the LexA-regulatedfor the open reading frame examined, the original identifica- genes, the level and timing of the induction observedtion numbers of Blattner, b#### (Blattner et al. 1997), were
in our experiments are in good agreement with previousused.observations. In confirmation of previous studies, weRaw data: The raw data from these experiments are avail-
able for download at the following web address http://www2. find that recN, recA, and sulA are heavily induced withinmsstate.edu/zjcc129. the first 5 min of irradiation whereas the uvrD induction
is much less robust (Casaregola et al. 1982; Arthurand Eastlake 1983; Salles and Paoletti 1983; Pick-
RESULTS AND DISCUSSIONsley et al. 1984; Sandler 1994). umuCumuD are alsoknown to be strongly induced; however, full inductionWe examined the response of E. coli strain MG1655
following a dose of 40 J/m2 (254 nm). Previous studies of these genes is not observed until 20 min after UVirradiation (Woodgate and Ennis 1991). We were un-in our laboratory have shown that exposing an exponen-
tially growing culture of E. coli to 40 J/m2 of UV produces able to assay ftsK induction in wild-type cells due toa problem amplifying the ftsK fragment when con-approximately one cyclobutane pyrimidine dimer on
each strand per 6 kb of DNA (Mellon and Hanawalt structing the bacterial microarray. However, some lexA-dependent induction is observed in lolA, possibly repre-1989; Crowley and Hanawalt 1998). This dose tran-
siently inhibits both replication and transcription, and senting some transcriptional readthrough from the ftsKgene. In some cases, we observed co-upregulation ofinduces a strong SOS response (Courcelle et al. 1997;
Crowley and Hanawalt 1998). More than half of the the neighboring ORFs that are transcribed in the sameorientation. This effect can clearly be seen in the induc-cells survive and genomic replication fully recovers
within z45 min following UV irradiation. Within that tion of dinB transcription, which also renders an in-crease in yafN, yafO, and yafP mRNA. Similarly, yebF andtime, most of the DNA lesions have also been repaired
(Mellon and Hanawalt 1989; Courcelle et al. 1999). yebE are also induced along with LexA-regulated yebG.In the case of recN, the downstream genes smpA and smpBTo examine the changes in gene expression in re-
sponse to this dose of UV irradiation, we compared also appear to be upregulated following UV irradiation.However, for b2619 and b2618 it is actually the antisensesamples of total RNA taken 5, 10, 20, 40, and 60 min after
irradiation to samples made just prior to irradiation. To strand that would be transcribed following UV irradia-tion if this induction represents transcriptional read-control for UV-independent changes, total RNA prepa-
rations from nonirradiated samples at 20 and 60 min through. The actual mechanism of such coregulationcould be produced by: (1) transcriptional readthroughwere also prepared. This analysis was carried out with
the wild-type MG1655 strain as well as the isogenic lexA1 resulting from inefficient transcriptional termination;(2) the actual operon spanning across the entire groupderivative and represents the changes in transcript levels
of each gene from up to seven independent comparative of neighboring genes; or (3) a regional effect conferredthrough protein factors or DNA structural conforma-hybridizations for each cell line, which were observed
within the same experiment. tions within the region under consideration.Some of the transcripts from documented LexA-regu-The average change in transcript level in the irradi-
ated samples compared to those in the unirradiated lated genes, dinG, molR, uvrD, and uvrA, did not signifi-cantly rise following UV irradiation. However, in eachsamples for each gene along the E. coli chromosome is
plotted sequentially in Figure 1. In some cases, no data of these cases, the samples of these transcripts in theunirradiated (control) culture were significantly de-were plotted for a gene, because either the PCR reaction
failed during microarray construction or the fluorescent creased during the time course. The reason for thisobservation is unclear. However, both initial and unirra-signal in the unirradiated samples was too low for reli-
able detection. However, raw data for any or all genes diated samples were “mock” UV treated by gentle agita-tion for 60 sec in a 15-cm glass petri dish and it isare available for downloading at the web addresses indi-
cated in materials and methods or upon request to possible that some genes were affected by this treatment.Importantly, however, when comparing the net changethe authors.
Genes induced in a LexA-dependent manner follow- in irradiated and unirradiated samples, the lexA-depen-dent induction of these genes is clearly evident: 1.77-,ing UV irradiation: Twenty-six functional LexA-binding
regions controlling at least 31 genes have been pre- 1.78-, 2.51-, and 3.85-fold increases, respectively.Of the reported LexA-regulated genes, we did notviously demonstrated to be functionally active following
irradiation. At the time at which these bacterial microar- detect significant induction of either hokE or ssb in ourexperiment. recA/lexA-dependent transcription fromrays were constructed, 3 of these genes, ysdAB, dinQ,
and dinS, had not yet been identified as open reading hokE has previously been shown to occur in the E. colistrain RW118 following mitomycin C treatment (Fer-frames (Fernandez De Henestrosa et al. 2000) and
were not included in our analysis. The time courses nandez De Henestrosa et al. 2000). However, theSOS induction of ssb is less clear. Although a plasmid-observed for all other genes/operons known to be regu-
lated by LexA and that contain LexA-binding sites are encoded ssb has been shown to be slightly upregulated
44 J. Courcelle et al.
Figure 1.—Changes in gene expression within the E. coli genome following UV irradiation. The average change in transcriptlevels in the irradiated samples compared to unirradiated samples for each gene along the E. coli chromosome is plottedsequentially. Open squares, wild type; solid circles, lexA1. The location of genes on the chromosome, in kilobase pairs, is indicatedalong the top of each graph. The average change in transcript levels was calculated as the (average change in irradiated samples)/(average change in unirradiated samples). The data for all plotted genes represent an average of between 3 and 5 irradiatedtime points and at least one unirradiated time point. Time points for which the PCR or hybridization failed, or the fluorescentsignal generated by the unirradiated sample was ,30% above the background level of fluorescence, were not included in theaverages.
45E. coli Gene Expression Profiles After UV
Figure 1.—Continued.
46 J. Courcelle et al.
Figure 1.—Continued.
47E. coli Gene Expression Profiles After UV
Figure 1.—Continued.
48 J. Courcelle et al.
Figure 1.—Continued.
49E. coli Gene Expression Profiles After UV
Figure 1.—Continued.
50 J. Courcelle et al.
51E. coli Gene Expression Profiles After UV
following SOS induction, no induction of the chromo- lation, or through other regulatory proteins that areinactivated by a similar RecA-catalyzed proteolysis. Thesomally encoded ssb has been reported and SOS induc-
tion does not lead to higher levels of SSB protein (Brand- activated form of RecA is also known to induce proteo-lytic cleavage of other proteins containing “LexA-like”sma et al. 1983; Perrino et al. 1987).
If the LexA-binding site is located within the operator cleavage motifs such as those found in UmuD, the plas-mid-encoded MucA, and the repressor proteins of sev-regions of two diverging transcripts, it is possible that
a single site may regulate the transcription of both oper- eral bacteriophage (Little 1984; Perry et al. 1985).This possibility is especially attractive considering thatons. This is presumed to be the case at uvrA and ssb
and also appears to occur between ybiA and dinG as well several of the newly identified genes, borD, the lit-intEregion, and ogrK, share homology with cryptic prophageas umuCD and hylE.
In addition to the previously reported lexA-regulated genes. The borD gene product is a homolog of the phagel Bor protein, a lipoprotein expressed during lysogenygenes, we observed several other genes that appeared
to be upregulated in a LexA/RecA-dependent manner that is present in the outer membrane. The borD geneproduct shares homology to other bacterial virulence(Figure 2B). However, to determine whether these
genes are directly under LexA control will require fur- proteins and its expression increases E. coli survival inanimal serum (Barondess and Beckwith 1990, 1995).ther investigation. Some of these genes do appear to
have potential candidate LexA boxes (Table 1B). One lit, intE, and several genes of unknown function inthis same region are expressed at relatively late timesmethod of predicting whether a LexA-like sequence will
bind LexA is to examine its heterology index (HI), following UV exposure (Figure 3). lit encodes a prote-ase specific for elongation factor EF-tu. Expression ofwhich is a value derived from a mathematical formula
ranking the relatedness of a potential sequence to that lit is induced at late times following phage T4 infectionand prevents late phase phage amplification throughof known LexA-binding sequences (Lewis et al. 1994).
Low HI values predict that a potential sequence is more its EF-tu proteolysis (Georgiou et al. 1998). FollowingT4 infection, the endogenous lit gene has been sug-likely to bind LexA protein. Previous studies found that
lexA sequences with an HI value of ,15 generally bound gested to trigger an apoptotic-like death of the infectedcell, thereby thwarting the reproduction of the virus andLexA (Lewis et al. 1994) and recently this method was
used to identify seven new lexA-regulated genes (Fer- precluding the widespead infection of the population.Further characterization is required to know whethernandez De Henestrosa et al. 2000). However, there
are exceptions to the predictions from HI values. On this activity or any of the genes in this region affectrecovery following DNA damage.the basis of earlier calculations that were based upon a
smaller set of lexA sequences, Fernandez De Henes- ogrK is a prophage gene from a phage P2. Ogr hasbeen shown to regulate late P2 gene transcriptiontrosa et al. (2000) found that although dinJ had an HI
value of 7.06, it did not bind LexA. Yet ybfE, which they through an interaction with the host RNA polymerase(Wood et al. 1997). Additionally, an ogr-like gene, regCcalculated to have an HI value of 14.07, did bind LexA
(Lewis et al. 1994). This observation suggests that all in Serratia marcescens, has been shown to be inducedfollowing mitomycin C treatment in an SOS-dependentfactors comprising a functional LexA box have not yet
been identified. Therefore, we have recalculated the HI manner (Jin et al. 1996).grxA is a glutoredoxin that acts as a hydrogen donorvalues using all 28 functional LexA sequences found on
the chromosome and we have included any potential for the E. coli ribonucleotide reductases. Several thiore-doxin and glutoredoxin genes in E. coli are coregulatedLexA-binding sequence with an HI value of ,20 in
Table 1B. with ribonucleotide reductase gene expression (Prieto-Alamo et al. 2000). From this perspective, it is interestingWhile some of these newly identified genes appear
to have potential LexA-binding sequences, many of the to note that the ribonucleotide reductase genes nrdAand nrdB are among the strongest lexA-independentinduced genes do not, suggesting that in some cases
the regulation may occur indirectly. Indirect lexA-depen- induced genes following UV exposure (Figure 4). grxAis also induced in an oxyR-dependent manner underdent induction of these genes might occur through
regulatory proteins that are themselves under lexA regu- some conditions (Prieto-Alamo et al. 2000).
Figure 2.—Transcriptional induction following UV irradiation in the genes surrounding known LexA boxes. The change intranscript levels for the indicated gene is plotted over time. The arrows indicate the direction of transcription within the operonrelative to the LexA box. Arrows pointing left are transcribed on the minus strand and arrows pointing right are transcribed onthe plus strand. The locations and distances, in base pairs, of the LexA box from the initial ATG codon are indicated in theboxes. The graphs of genes that are directly adjacent on the chromosome are joined together. The location of the gene(s) onthe chromosome, in kilobase pairs, is indicated along the top of each plot. Solid squares, irradiated wild type; open squares,unirradiated wild type; solid circles, irradiated lexA1; open circles, unirradiated lexA1. Time points in which the PCR or hybridizationfailed, or the fluorescent signal generated by the unirradiated sample was ,30% above the background level of fluorescence,are not plotted.
52 J. Courcelle et al.
TABLE 1 TABLE 1
Known and potential LexA boxes surrounding induced genes (Continued)
HI BasesA. Known genes LexA box sequence valuea HI from
B. Potential LexA box valueb startysdAB tactgtttatttatacagta 1.81umuDC tactgtatataaaaacagta 2.12 intE regionsbmC tactgtatataaaaacagta 2.12 intE ggctgctgaaaaatacagaa 16.94 2195pcsA aactgtatataaatacagtt 2.19 ymfI ttctgtaccagaaaacagtt 15.48 84recN no. 1 tactgtatataaaaccagtt 3.53 ymfM agctgcaggagcatgcagca 19.32 2122dinQ tactgtatgattatccagtt 3.92 lit tgatgacagagtgtccagtg 20.32 2193urvB aactgtttttttatccagta 4.26 ymfE cactggacactctgtcatca 20.32 2280dinI acctgtataaataaccagta 4.84 intE ggcggtataagcatccagtg 14.76 84hokE cactgtataaataaacagct 4.92 intE tgctgaaaaatacagaagta 20.81 2192recA tactgtatgctcatacagta 4.98 ymfM ggcagttattcaaaacagat 19.98 2222sulA tactgtacatccatacagta 5.39 ymfM aaccgcatgagaagacagca 18.91 2173uvrA tactgtatattcattcaggt 6.23 ymfN aactgattgcgcttcctgta 16.89 2312ssb acctgaatgaatatacagta 6.23 ymfN cgctggttcaaagatcacta 20.90 2152yebG tactgtataaaatcacagtt 6.26 ymgF regionlexA/denF no. 2 aactgtatatacacccaggg 7.25 ymgF cggtgtaattatagacagct 15.08 2105ydjQ cactggatagataaccagca 7.42 ymgH aactgaaaaaactccccggg 19.13 6lexA/dinF no. 1 tgctgtatatactcacagca 7.45 ydeO regionruvAB cgctggatatctatccagca 7.59 ydeO aaatgcatgcgaccacagtg 20.68 2272yjiW tactgatgatatatacaggt 7.92 ydeT regionmolR aactggataaaattacaggg 8.14 ydeS tactgaaccagcagacagca 16.79 243dinS agctgtatttgtctccagta 8.24 yneL cactgcatacgaaaacacca 18.21 257uvrD atctgtatatatacccagct 8.46 yoaA regionrecN no. 2 tactgtacacaataacagta 8.50 yoaB ccctgttgatttgaacaggg 13.32 2123dinG tattggctgtttatacagta 8.65 yoaA ccctgttcaaatcaacaggg 13.32 224yigN aactggacgtttgtacagca 8.82 ogrK regionydjM1 tactgtacgtatcgacagtt 9.05 ogrK cattgtcctttatgccagca 19.29 8ftsK tcctgttaatccatacagca 9.18 ogrK gactggacaatcactaaggt 19.35 2193dinB cactgtatactttaccagtg 9.40 yqgC regionrecN no. 3 taatggtttttcatacagga 10.08 yqgC acatggattttccagcagtg 18.78 2193ydjM2 cactgtataaaaatcctata 10.85 yqgC ctcagtaactgtaaccagct 20.65 241ybfE aactgattaaaaacccagcg 10.92 yhiL regionpolB gactgtataaaaccacagcc 12.55 yhiL atctgtttttcagacaagta 18.22 263
yhiL tgctgttgttttttacaatt 12.30 2187Concensus taCTGtatatatataCAGta glvB region
glvG tcctgaagtggcattcagcg 17.45 211(continued) glvG taatgaccaaattctcagtg 19.17 0
glvB tgctggtgggaattaccgaa 20.04 2174glvC ggctggccaaaagtacaaat 20.85 578glvC tgctgtcggtttacccattg 15.97 214glvB induction is unusual in that glvB lies in the mid-
ipbA regiondle of a predicted operon and encodes a portion of aibpA tgctgaaaataacatcatca 17.25 2249protein transport system. Nevertheless, glvB induction
yigN regionwas also observed following exposure to gamma irradia- yigN aactggacgtttgtacagca 8.82 261tion (data not shown) and may be driven from an alter-
a HI values were calculated from all sequences reported bynative promoter or alternative open reading frame inLewis et al. (1994) and Fernandez de Henestrosa et al.the region.(2000). The HI values reported here were calculated to in-
In the case of yigN, a previous study has demonstrated clude the results of Fernandez de Henestrosa et al. (2000)that it contains a functional LexA binding site; however, and therefore differ from the values used in their previous
study.no further increase in yigN expression was observedb No sequences with HI values ,20 were found for grxA,following treatment with mitomycin C in wild-type,
borD, ybiN, arpB, yccF, or yifL.lexA51 (deficient), or lexA1 (uninducible) E. coli cul-tures. We have no clear explanation of this difference.However, alternative promoters proximal to yigN could ibpA (hslT) and ibpB (hslS), encoding heat-induciblehave allowed for full expression to occur in these previ- chaperonins, were also induced in a LexA-dependentous studies prior to mitomycin treatment since yigN manner.appeared to be heavily expressed under all conditions There has been little functional characterization of
the remaining induced genes. yoaA shares homologyin that study (Fernandez De Henestrosa et al. 2000).
53E. coli Gene Expression Profiles After UV
Figure 3.—Genes that displayed the largest LexA-dependent transcriptional induction following UV irradiation are plotted.The change in transcript levels for the indicated gene is plotted as in Figure 2. Solid squares, irradiated wild type; open squares,unirradiated wild type; solid circles, irradiated lexA1; open circles, unirradiated lexA1.
54 J. Courcelle et al.
Figure 4.—Representation of genes dis-playing a LexA-independent transcription-al induction following UV irradiation. Thechange in transcript levels for the indicatedgene is plotted as in Figure 2. (A) Thelargest LexA-independent inductions. (B)Typical profiles of genes with an early UV-dependent transcriptional induction. (C)Typical profiles of genes with a slow UV-dependent transcriptional induction. Solidsquares, irradiated wild type; open squares,unirradiated wild type; solid circles, irradi-ated lexA1; open circles, unirradiated lexA1.
with other ATP-dependent helicases. The gene products ularly impressive considering that these nucleotide me-tabolism genes are often found in very small operonsof ydeT, ydeS, and ydeR share homology to other fimbrial
proteins. b1169 ycgH has homology with other ATP-bind- spaced throughout the genome. Other categories ofgenes that appeared to be upregulated included heat-ing subunits of transport systems. Both ydeO and ydiW
have motifs that suggest they may function as transcrip- shock or chaperone proteins as well as several of thegenes involved in RNA metabolism. It is notable thattional regulators. No significant homology between
ybiN, yqgC, yhiJL, or yifL and any other characterized nearly half of the genes that were upregulated have hadlittle or no functional characterization.proteins has been reported.
Genes induced independently of LexA following UV Loss of gene expression following UV irradiation:Whereas several studies have focused upon the need toirradiation: The time courses of the largest lexA-inde-
pendent inductions are plotted in Figure 4A. Most strik- upregulate certain gene products following UV irradia-tion, it has remained relatively unexplored, yet very pos-ing is precisely how few lexA-independent changes occur
following UV exposure. In general, lexA-independent sible, that repression or even active degradation of somegene transcripts will also be an important factor in cellu-inductions, with the exception of nrdA, nrdB, and yeeF,
are in the range of twofold effects. Furthermore, many lar recovery. The bacterial microarray offers an opportu-nity to address this very question. Indeed, repressionof these lexA-independent profiles appear to rise very
rapidly (within the first 5 min) and then either subside was observed in a large number of genes following UVirradiation. However, our results do not allow us toor plateau. A large number of genes and regions were
observed to be regulated in this manner and some gen- determine whether the decrease in a given transcriptrepresents diminished transcription or accelerated deg-eralizations are apparent from both Figure 1 and Table
2. Many proteins associated with the replication machin- radation in response to UV irradiation. Nevertheless, alarge number of genes in the wild-type, but not in theery are slightly induced following UV irradiation. Addi-
tionally, several genes associated with purine and pyrimi- lexA1, samples were reduced in their transcript levels atthe 5-, 10-, and 20-min time points following irradiation.dine metabolism seem to be upregulated in a similar
manner. Although not dramatic, these results are partic- This observation may suggest that some inhibition of
55E. coli Gene Expression Profiles After UV
TA
BL
E2
Gen
esw
ith
incr
ease
dtr
ansc
ript
leve
lsfo
llow
ing
UV
-irra
diat
ion
Wild
type
:m
inut
espo
stir
radi
atio
nc
lexA
1:m
inut
espo
stir
radi
atio
n
2060
2060
WT
lexA
1(N
o(N
o(N
o(N
oG
ene
(ave
)b(a
ve)
510
2040
60U
V)
UV
)5
1020
4060
UV
)U
V)
Poss
ible
fun
ctio
n
Rep
licat
ion
and
repa
irum
uCa
20.6
0.97
45.
2220
.59
15.5
839
.36
22.7
41.
110.
90.
950.
910.
950.
971.
041.
040.
94Po
lV,
SOS
mut
agen
esis
recN
a20
.18
0.93
728
.94
26.2
26.7
29.7
623
.07
1.36
1.31
0.79
0.8
0.85
0.9
0.76
0.99
0.76
Prot
ein
used
inD
NA
repa
irum
uDa
17.3
61.
046
5.13
12.4
228
.56
27.0
78
1.18
0.69
0.94
1.01
1.11
1.01
1.03
10.
95SO
Sm
utag
enes
is;
form
sco
mpl
exw
ith
PolV
recA
a10
.08
1.25
16.
166.
289.
268.
494.
570.
60.
781.
090.
950.
931.
041.
120.
80.
84H
omol
ogou
sst
ran
dpa
irin
g,D
NA
stra
nd
exch
ange
dinB
a7.
749
1.09
83.
665.
87.
085.
725.
250.
711.
031.
020.
810.
941.
030.
880.
88Po
lIV
uvrB
a4.
142
1.49
63.
164.
424
5.03
4.62
0.94
1.11
1.15
1.11
1.35
1.63
1.68
0.98
0.87
DN
Are
pair
;ex
cisi
onn
ucle
ase
subu
nit
Buv
rAa
3.84
61.
167
1.96
1.79
1.68
1.37
1.18
0.39
0.44
1.07
1.01
0.88
0.85
0.83
0.74
0.85
DN
Are
pair
;ex
cisi
onn
ucle
ase
subu
nit
Aru
vAa
3.55
21.
043
4.54
4.6
3.07
3.76
3.3
1.06
1.11
1.16
11.
11.
071.
21.
150.
97H
ollid
ayju
nct
ion
hel
icas
esu
bun
itB
;br
anch
mig
rati
onpo
lBa
3.2
1.09
81.
461.
71.
611.
652.
140.
520.
550.
910.
760.
730.
822.
190.
911.
06D
NA
poly
mer
ase
IIyd
jQa
3.36
10.
852
2.78
3.35
2.13
2.41
2.27
0.63
0.91
0.87
0.79
0.68
0.69
0.59
0.86
0.84
Puta
tive
exci
nuc
leas
esu
bun
ituv
rDa
2.50
51.
127
1.25
1.02
1.22
1.47
1.49
0.47
0.56
1.1
1.03
1.17
1.2
1.33
1.09
0.98
DN
Aex
cisi
onre
pair
;h
elic
ase
IIre
cF1.
792
1.67
51.
221.
10.
990.
981.
310.
590.
662.
011.
651.
110.
980.
910.
860.
73ss
DN
Aan
dds
DN
Abi
ndi
ng,
AT
Pbi
ndi
ng
dnaN
1.68
41.
591.
831.
461.
091.
051.
350.
810.
82.
251.
751.
61.
151.
081.
020.
95D
NA
poly
mer
ase
III,
b-s
ubun
itdn
aA1.
627
1.63
32.
451.
321.
591.
21.
370.
841.
112.
572.
071.
721.
351.
271.
031.
17D
NA
init
iati
onof
chro
mos
ome
repl
icat
ion
dnaC
1.48
21.
621
2.06
1.52
1.32
1.64
1.28
1.2
0.91
1.68
1.41
1.54
1.88
1.92
1.15
0.93
DN
Are
plic
atio
nin
itia
tion
and
chai
nel
onga
tion
rep
1.62
21.
433
1.13
0.83
0.8
1.1
1.33
0.57
0.71
1.67
1.53
1.56
1.68
1.91
1.14
1.19
Rep
hel
icas
e,ch
rom
osom
ere
plic
atio
nru
vBa
1.93
10.
889
3.19
2.96
2.66
2.78
2.22
1.42
1.44
1.01
1.01
1.01
1.02
0.86
1.09
1.12
Hol
liday
jun
ctio
nh
elic
ase
subu
nit
A;
bran
chm
igra
tion
ruvC
1.37
51.
452
1.01
0.76
0.89
0.81
0.62
0.5
0.69
1.58
1.51
1.55
1.49
1.64
1.16
0.98
Hol
liday
jun
ctio
nn
ucle
ase;
reso
luti
onof
stru
ctur
es
Tra
nsc
ript
ion
and
tran
scri
ptio
nal
regu
lati
onle
xAa
4.8
0.91
43.
213.
073.
082.
772.
510.
610.
610.
840.
60.
670.
60.
490.
780.
62R
egul
ator
for
SOS(
lexA
)re
gulo
ndi
nIa
4.46
11.
022.
462.
813.
242.
781.
980.
490.
71.
041
1.06
1.1
0.9
0.97
1.03
Dam
age-
indu
cibl
epr
otei
nI
deaD
1.47
92.
819
1.31
0.65
0.85
0.64
0.58
0.5
0.59
2.11
1.35
1.62
1.7
2.1
0.65
0.61
Indu
cibl
eA
TP-
inde
pen
den
tR
NA
hel
icas
erp
oD1.
712.
131
2.33
1.84
1.36
1.43
0.95
0.87
0.98
2.78
2.73
2.41
2.43
2.86
1.28
1.2
RN
Apo
lym
eras
e,si
gma(
70)
fact
orhe
pA1.
92N
D1.
841.
821.
772.
161.
530.
891.
01Pr
obab
leA
TP-
depe
nde
nt
RN
Ah
elic
ase
fisa
2.29
41.
366
3.02
2.19
1.94
2.01
1.22
0.83
0.98
1.63
1.43
1.56
1.44
1.52
1.05
1.17
DN
Ain
vers
ion
fact
or,
tran
scri
ptio
nfa
ctor
suhB
a2.
081
1.55
51.
941.
331.
351.
60.
960.
690.
692.
382.
072.
252.
562.
711.
441.
64E
nh
ance
ssy
nth
esis
ofs
32in
mut
ant
ttka
2.17
91.
408
2.67
2.07
1.77
2.56
1.77
1.09
0.9
1.4
1.52
1.58
1.44
1.17
0.94
Puta
tive
tran
scri
ptio
nal
regu
lato
ryd
eOa
2.41
21.
009
1.64
3.37
10.3
32.
981.
581.
651.
131.
111.
191.
231.
321.
181.
19Pu
tati
veA
RA
C-ty
pere
gula
tory
prot
ein
rph
1.75
1.59
51.
531.
080.
821.
41.
250.
690.
71.
691.
661.
762.
041.
821.
221.
03R
Nas
ePH
srm
B1.
474
1.83
91.
961.
421.
161.
541.
290.
881.
122.
782.
42.
32.
492.
721.
311.
45A
TP-
depe
nde
nt
RN
Ah
elic
ase
soxS
1.72
81.
345
2.07
1.48
2.1
0.95
1.06
0.85
1.06
1.1
1.23
1.48
1.05
0.93
0.83
Reg
ulat
ion
ofsu
pero
xide
resp
onse
regu
lon
rnpA
1.69
61.
329
2.32
1.47
1.24
1.34
1.05
0.81
0.94
1.45
1.28
1.24
1.29
1.45
0.94
1.08
RN
ase
Pco
mpo
nen
t;pr
oces
ses
tRN
A,
4.5S
RN
A
(con
tinue
d)
56 J. Courcelle et al.
TA
BL
E2
(Con
tinu
ed)
Wild
type
:m
inut
espo
stir
radi
atio
nc
lexA
1:m
inut
espo
stir
radi
atio
n
2060
2060
WT
lexA
1(N
o(N
o(N
o(N
oG
ene
(ave
)b(a
ve)
510
2040
60U
V)
UV
)5
1020
4060
UV
)U
V)
Poss
ible
fun
ctio
n
Nuc
leos
ide
met
abol
ism
nrdA
2.05
15.
046
2.11
2.06
3.15
8.28
6.5
2.37
1.94
1.06
1.66
4.91
11.7
420
.49
1.77
1.39
Rib
onuc
leos
ide
redu
ctas
e1,
a-s
ubun
it,
B1
grxA
a4.
515
1.20
52.
1825
.25
9.65
1.9
1.2
1.66
1.9
1.07
0.91
11.
061.
230.
950.
8G
luta
redo
xin
coen
zym
efo
rri
bon
ucle
otid
ere
duct
ase
nrdB
2.11
72.
956
1.4
1.26
2.51
5.92
4.47
1.53
1.41
0.81
1.05
2.25
5.23
7.14
1.15
1.08
Rib
onuc
leos
ide
redu
ctas
e1,
b-s
ubun
it,
B2
upp
2.12
61.
922
14.4
59.
437.
348.
623.
323.
934.
194
3.53
2.26
2.63
2.76
1.53
1.63
Ura
cil
phos
phor
ibos
yltr
ansf
eras
epy
rF1.
734
1.70
12.
131.
971.
22.
662.
11.
11.
221.
961.
571.
491.
761.
980.
931.
13O
roti
din
e-59
-ph
osph
ate
deca
rbox
ylas
ets
x1.
964
1.33
14.
082.
341.
612.
121.
240.
931.
391.
721.
511.
421.
261.
211.
051.
09N
ucle
osid
ech
ann
el;
phag
eT
6re
cept
oran
dco
licin
Kgu
aA1.
833
1.44
72.
041.
891.
082.
091.
470.
910.
961.
721.
891.
51.
61.
611.
051.
25G
MP
syn
thet
ase
(glu
tam
ine-
hyd
roly
zin
g)sp
eB1.
494
1.75
71.
131.
060.
890.
880.
970.
620.
71.
681.
491.
811.
751.
660.
920.
99A
gmat
inas
epu
rF1.
728
1.51
53.
132.
371.
273.
242.
171.
311.
512.
51.
91.
611.
671.
561.
141.
3PR
PPam
inot
ran
sfer
ase
dfp
1.60
11.
602
2.9
1.95
1.96
2.19
2.65
1.41
1.5
2.06
1.62
1.8
1.78
1.75
1.29
0.96
Flav
opro
tein
affe
ctin
gD
NA
pan
thot
hen
ate
met
abol
ism
pyrH
1.60
21.
562.
361.
331.
131.
81.
230.
851.
111.
711.
531.
721.
561.
011.
08U
ridy
late
kin
ase
ntpA
1.41
61.
732
1.54
1.53
1.25
1.76
1.39
0.92
1.19
1.55
1.79
1.8
1.88
1.9
11.
06dA
TP
pyro
phos
phoh
ydro
lase
dut
1.64
11.
504
1.68
1.28
0.95
1.42
1.48
0.84
0.82
1.36
1.43
1.5
1.55
1.64
1.06
0.93
Deo
xyur
idin
etri
phos
phat
ase
gauB
1.50
91.
532
2.64
1.76
1.53
2.33
1.81
1.23
1.44
2.02
1.98
1.75
1.97
1.51
1.21
1.2
IMP
deh
ydro
gen
ase
purB
1.47
91.
526
3.31
2.82
2.39
3.38
2.26
1.49
2.34
2.14
2.2
1.86
2.18
1.92
1.36
1.34
Ade
nyl
osuc
cin
ate
lyas
egp
t1.
666
1.31
92.
852.
012
1.9
1.03
1.09
1.26
1.67
1.51
1.36
1.48
1.4
1.01
1.24
Gua
nin
e-h
ypox
anth
ine
phos
phor
ibos
yltr
ansf
eras
epy
rD1.
557
1.42
68.
045.
092.
985.
82.
732.
763.
572.
021.
71.
171.
291.
21.
011.
06D
ihyd
ro-o
rota
tede
hyd
roge
nas
epu
rH1.
494
1.47
80.
720.
930.
491.
511.
730.
580.
861.
651.
551.
81.
681.
121.
14A
ICA
Rfo
rmyl
tran
sfer
ase;
IMP
cycl
ohyd
rola
sepy
rE1.
839
1.12
41.
381.
060.
851.
31.
250.
60.
671.
131.
060.
921.
020.
930.
940.
86O
rota
teph
osph
orib
osyl
tran
sfer
ase
mur
B1.
457
1.43
83.
182.
012.
352.
682.
61.
631.
891.
21.
171.
251.
331.
090.
870.
81U
DP-
N-a
cety
len
olpy
ruvo
ylgl
ucos
amin
ere
duct
ase
cmk
1.5
1.37
1.69
1.8
0.99
2.18
1.48
1.24
0.93
1.48
1.46
1.37
1.46
1.39
1.08
1.01
Cyt
idyl
atat
eki
nas
ekd
sB1.
623
1.22
50.
821.
110.
661.
851.
320.
70.
721
1.15
0.81
1.05
0.95
0.85
0.77
CT
P:C
MP-
3deo
xy-d
-man
no-
octu
loso
nat
etr
ansf
eras
e
Tra
nsl
atio
n/a
min
oac
idm
etab
olis
mar
gS1.
708
1.64
52.
512.
81.
593.
362.
551.
671.
331.
861.
71.
461.
831.
911.
131
Arg
inin
etR
NA
syn
thet
ase
prfC
1.65
61.
576
2.01
1.49
1.28
1.75
1.79
0.98
1.03
1.98
1.58
1.68
1.9
21.
11.
22Pe
ptid
ech
ain
rele
ase
fact
orR
F-3
aspS
1.66
21.
542.
131.
651.
271.
531.
691.
010.
982.
191.
822.
042.
152.
041.
381.
28A
spar
tate
tRN
Asy
nth
etas
esp
eA1.
485
1.71
51.
621.
491.
11.
261.
250.
870.
942.
122.
241.
761.
871.
71.
031.
23B
iosy
nth
etic
argi
nin
ede
carb
oxyl
ase
prfB
1.59
81.
594
1.97
1.39
1.37
1.73
2.13
0.97
1.18
1.6
1.62
1.59
1.67
1.45
0.96
1.03
Pept
ide
chai
nre
leas
efa
ctor
RF-
2fa
bZ1.
698
1.49
23.
632.
72.
712.
941.
821.
641.
611.
511.
461.
51.
661.
591.
041.
03(3
R)-
hyd
roxy
myr
isto
lac
ylca
rrie
rde
hyd
rata
setg
t1.
682
1.50
72.
21.
651.
641.
961.
591.
071.
081.
91.
841.
861.
91.
691.
21.
24tR
NA
-gua
nin
etr
ansg
lyco
syla
seyj
eA1.
759
1.29
81.
851.
631.
141.
40.
930.
950.
631.
581.
391.
451.
451.
431.
051.
2Pu
tati
vely
syl-t
RN
Asy
nth
etas
egl
tX1.
671.
375
3.65
2.84
1.88
3.49
2.67
1.95
1.53
1.68
1.67
1.6
1.97
2.05
1.2
1.41
Glu
tam
ate
tRN
Asy
nth
etas
e,ca
taly
tic
subu
nit
queA
1.61
31.
381
1.22
0.84
0.83
1.05
0.9
0.61
0.59
1.8
1.5
1.55
1.58
1.82
1.14
1.25
Syn
thes
isof
queu
ine
intR
NA
yafT
a1.
747
1.12
31.
161.
151.
91.
730.
960.
890.
691.
161.
051.
141.
341.
151.
011.
07Pu
tati
veam
inop
epti
dase
(con
tinue
d)
57E. coli Gene Expression Profiles After UV
TA
BL
E2
(Con
tinu
ed)
Wild
type
:m
inut
espo
stir
radi
atio
nc
lexA
1:m
inut
espo
stir
radi
atio
n
2060
2060
WT
lexA
1(N
o(N
o(N
o(N
oG
ene
(ave
)b(a
ve)
510
2040
60U
V)
UV
)5
1020
4060
UV
)U
V)
Poss
ible
fun
ctio
n
Hea
tsh
ock,
tran
spor
tpr
otei
ns
ycgH
a5.
823
1.08
64.
1620
.67
10.3
72.
071.
291.
911.
131.
081.
121.
171.
581.
041.
2Pu
tati
veA
TP-
bin
din
gtr
ansp
ort
syst
emco
mpo
nen
tgl
vBa
5.73
70.
902
1.65
3.69
4.64
3.84
3.82
0.74
0.49
1.05
1.08
11.
10.
911.
111.
17PT
Ssy
stem
,ar
buti
n-li
keII
Bco
mpo
nen
tye
eF3.
086
2.81
56.
085.
672.
973.
51.
221.
251.
274.
983.
82.
872.
442.
381.
171.
17Pu
tati
veam
ino
acid
/am
ine
tran
spor
tpr
otei
nyb
eWa
2.98
60.
913
0.9
1.76
8.27
1.97
1.08
0.84
0.9
1.03
1.12
1.04
0.96
1.2
Puta
tive
dnaK
prot
ein
ibpB
*2.
216
1.33
52.
992.
712.
593.
161.
91.
281.
131.
191.
241.
261.
391.
561.
090.
9H
eat-s
hoc
kpr
otei
nco
rA1.
805
1.63
1.88
1.37
1.15
2.21
2.01
0.98
0.93
2.39
2.04
2.08
2.52
2.38
1.43
1.37
Mg2 1
tran
spor
t,sy
stem
Iyh
fC1.
771
1.57
32.
112.
011.
272.
221.
511.
031.
032.
271.
61.
811.
791.
771.
141.
21Pu
tati
vetr
ansp
ort
sdaC
1.76
21.
384
1.82
1.85
0.72
1.89
1.43
1.17
0.58
1.7
1.6
1.59
1.54
1.7
1.26
1.09
Prob
able
seri
ne
tran
spor
ter
potB
a1.
833
1.22
64.
543.
131.
982.
772.
061.
541.
621.
761.
291.
041.
091.
010.
971.
05Sp
erm
idin
e/pu
tres
cin
etr
ansp
ort
syst
empe
rmea
sehs
lU1.
559
1.49
81.
641.
731.
412.
072.
541.
211.
21.
241.
792.
12.
022.
511.
411.
17H
eat-s
hoc
kpr
otei
nh
slV
U,
AT
Pase
subu
nit
potC
1.50
11.
489
4.53
3.66
1.75
2.61
2.05
1.82
2.07
2.44
2.02
1.34
1.26
1.28
1.01
1.23
Sper
mid
ine/
putr
esci
ne
tran
spor
tsy
stem
perm
ease
uraA
1.55
41.
382.
852.
140.
881.
650.
990.
821.
372.
372.
051.
151.
311.
161.
061.
27U
raci
ltr
ansp
ort
potD
1.38
31.
498
2.03
2.3
1.99
1.58
1.23
1.24
1.4
1.98
2.69
2.23
2.09
1.72
1.5
1.36
Sper
mid
ine/
putr
esci
ne
peri
plas
mic
tran
spor
tpr
otei
npo
tA1.
611.
241
4.43
3.36
1.75
2.51
1.47
1.98
1.38
1.74
1.82
1.38
1.19
1.16
1.06
1.29
AT
P-bi
ndi
ng
com
pon
ent
ofsp
erm
idin
etr
ansp
ort
artP
1.50
31.
305
3.15
2.89
1.43
2.92
1.52
1.75
1.42
1.75
1.58
1.32
1.64
1.54
1.28
1.12
Th
ird
argi
nin
etr
ansp
ort
syst
em,
AT
P-bi
ndi
ng
Cel
lD
ivis
ion
sulA
*9.
561
1.10
813
.74
11.7
13.1
711
.55
9.36
1.05
1.44
0.85
0.92
0.76
0.9
0.89
0.89
0.67
Supp
ress
orof
lon
;in
hib
its
cell
divi
sion
Prop
hag
ege
nes
ymfN
a7.
571.
034
0.09
3.35
7.12
0.54
0.39
1.1
1.03
1.14
1.1
0.93
1.15
0.9
Orf
,h
ypot
het
ical
prot
ein
intE
a4.
292
0.90
51.
051.
171.
767.
9621
.11
1.65
1.43
0.91
0.96
0.95
1.01
1.15
1.03
1.17
Prop
hag
ee1
4in
tegr
ase
ymfJ
a3.
658
1.00
40.
71.
021.
1713
.56
4.95
1.17
1.03
0.9
0.94
0.96
0.94
10.
9O
rf,
hyp
oth
etic
alpr
otei
nym
fGa
2.51
40.
996
0.75
1.31
1.05
4.5
6.28
1.1
1.11
0.98
1.04
1.03
1.12
1.01
1.05
1.03
Orf
,h
ypot
het
ical
prot
ein
ogrK
a2.
191
1.24
22.
984.
76.
893.
231.
591.
691.
851.
121.
111.
142
1.09
0.94
1.14
Prop
hag
eP2
ogr
prot
ein
ybcU
a1.
854
1.00
49.
355.
63.
685.
152.
972.
613.
161.
161.
051.
021.
031.
011.
021.
08B
acte
riop
hag
el
Bor
prot
ein
hom
olog
Oth
ers
prfB
2.15
9N
D1.
961.
411.
241.
732.
080.
78fa
bF1.
788
2.24
93.
052.
232.
532.
731.
81.
381.
381.
81.
891.
972.
242.
951.
020.
913-
oxoa
cyl-[
acyl
-car
rier
-pro
tein
]sy
nth
ase
IIpp
hB2.
743
1.18
92.
183.
188.
51.
291.
241.
31.
091.
111.
021.
011.
071.
080.
940.
84Pr
otei
nph
osph
atas
e2
yhdG
2.08
71.
744
1.83
1.59
1.24
1.66
0.88
0.68
0.7
2.38
2.01
2.13
1.93
1.84
1.18
1.18
Puta
tive
deh
ydro
gen
ase
hlyE
1.89
4N
D2.
522.
974.
353.
081.
571.
281.
78H
emol
ysin
Eri
bH1.
857
1.70
31.
140.
990.
81.
11.
170.
410.
711.
641.
571.
481.
61.
630.
930.
93R
ibofl
avin
syn
thas
e,b
chai
ngi
dA1.
678
1.55
81.
140.
870.
780.
931.
020.
520.
611.
391.
421.
651.
461.
440.
831.
06G
luco
se-in
hib
ited
divi
sion
;ch
rom
osom
ere
plic
atio
n?
prm
A1.
595
ND
1.29
1.18
1.04
1.31
1.12
0.63
0.86
cvpA
1.79
11.
368
3.05
3.15
1.77
4.85
2.67
2.03
1.43
1.61
1.31
1.29
1.44
1.19
0.94
1.06
Mem
bran
epr
otei
nre
quir
edfo
rco
licin
Vpr
oduc
tion
pabC
1.55
5N
D1.
251.
191.
251.
571.
270.
840.
844-
amin
o-4-
deox
ych
oris
mat
ely
ase
(con
tinue
d)
58 J. Courcelle et al.
TA
BL
E2
(Con
tinu
ed)
Wild
type
:m
inut
espo
stir
radi
atio
nc
lexA
1:m
inut
espo
stir
radi
atio
n
2060
2060
WT
lexA
1(N
o(N
o(N
o(N
oG
ene
(ave
)b(a
ve)
510
2040
60U
V)
UV
)5
1020
4060
UV
)U
V)
Poss
ible
fun
ctio
n
Oth
ers
(con
tinue
d)pt
a1.
661.
444
1.72
1.73
1.14
2.57
2.26
1.26
1.01
1.47
1.73
1.76
1.99
2.11
1.2
1.31
Phos
phot
ran
sace
tyla
senu
oB1.
567
1.49
22.
112.
461.
233.
122.
481.
511.
42.
171.
481.
531.
481.
321.
091.
05N
AD
Hde
hyd
roge
nas
eI
chai
nB
gidB
1.69
81.
354
2.08
1.4
1.79
1.7
1.52
0.85
1.15
1.35
1.3
1.39
1.31
1.35
10.
98G
luco
se-in
hib
ited
divi
sion
;ch
rom
osom
ere
plic
atio
n?
fldA
1.49
11.
474
5.95
4.41
4.5
5.5
3.64
3.29
3.15
1.8
1.51
1.68
2.11
2.22
1.17
1.36
Flav
odox
in1
plsX
1.59
41.
363
2.01
1.37
1.1
1.8
1.33
0.99
0.92
1.48
1.32
1.31
1.5
1.41
1.04
1.02
Gly
cero
lph
osph
ate
auxo
trop
hy
inpl
sBba
ckgr
oun
dsm
pAa
1.95
0.98
42.
152.
052.
61.
961.
671
1.14
1.03
1.01
0.94
0.86
0.93
0.94
1Sm
all
mem
bran
epr
otei
nA
smpB
a1.
755
1.16
92.
642.
331.
672.
391.
811.
281.
191.
231.
491.
231.
281.
231.
081.
13Sm
all
prot
ein
Bem
rB1.
606
1.28
61.
281.
061.
041.
151.
050.
650.
741.
321.
061.
161.
430.
981.
050.
8M
ulti
drug
resi
stan
ce;
puta
tive
tran
sloc
ase
ackA
1.54
11.
342
3.41
2.91
2.97
3.27
2.62
1.92
2.02
1.23
1.34
1.25
1.37
1.52
0.99
1.01
Act
ate
kin
ase
fabG
1.26
51.
576
2.13
1.84
1.86
2.04
1.27
1.3
1.59
1.24
1.44
1.47
1.72
2.01
0.94
1.06
3-ox
oacy
l-[ac
yl-c
arri
er-p
rote
in]
redu
ctas
esb
p1.
344
1.48
10.
840.
811.
143.
663.
361.
471.
450.
61.
11.
62.
212.
971.
181.
11Pe
ripl
asm
icsu
lfat
e-bi
ndi
ng
prot
ein
Un
know
ns
dinD
a10
.47
1.02
86.
715.
956.
025.
486.
190.
560.
60.
770.
720.
570.
710.
520.
780.
5D
NA
-dam
age-
indu
cibl
epr
otei
nor
aAa
9.00
21.
087
4.83
5.99
6.2
8.43
3.13
0.67
0.6
1.09
1.05
1.08
1.04
1.04
0.97
0.98
Reg
ulat
or,
Ora
Apr
otei
nye
bGa
8.85
31.
175
3.87
4.51
5.64
6.1
3.34
0.44
0.62
0.95
0.82
0.75
0.84
0.87
0.67
0.77
Orf
,h
ypot
het
ical
prot
ein
yfaE
2.18
2.69
10.
861.
474.
093.
481.
190.
810.
770.
941.
783.
614.
670.
870.
88O
rf,
hyp
oth
etic
alpr
otei
nyi
gFa
3.81
31.
057
1.84
15.1
83.
022.
031.
191.
221.
090.
980.
971.
081.
061.
020.
94O
rf,
hyp
oth
etic
alpr
otei
nyi
gNa
3.96
90.
866
2.11
2.38
2.13
3.13
4.14
0.66
0.74
0.79
0.82
0.86
0.76
0.71
0.89
0.93
Puta
tive
a-h
elix
chai
nar
pBa
3.74
90.
996
2.29
12.2
95.
322.
581.
611.
231.
341.
081.
010.
950.
940.
80.
970.
95O
rf,
hyp
oth
etic
alpr
otei
ndi
nFa
3.62
11.
029
2.1
1.98
1.26
1.81
1.54
0.58
0.38
1.02
1.06
0.87
0.84
0.84
0.95
0.85
DN
A-d
amag
e-in
duci
ble
prot
ein
Fya
fOa
3.48
61.
031
3.73
4.97
3.51
3.35
2.83
0.8
1.31
0.98
0.96
0.86
0.96
1.11
1.02
0.87
Orf
,h
ypot
het
ical
prot
ein
yegQ
2.03
42.
403
2.32
1.85
0.86
1.63
1.02
0.63
0.88
3.66
3.18
2.53
2.35
2.46
1.18
1.18
Orf
,h
ypot
het
ical
prot
ein
yoaA
2.18
2N
D1.
431.
21.
081.
431.
350.
60.
59Pu
tati
veen
zym
eya
fNa
2.73
81.
097
33.
713.
662.
281.
051.
261.
011.
080.
950.
820.
920.
84O
rf,
hyp
oth
etic
alpr
otei
nye
bFa
2.90
90.
859
3.24
4.06
3.33
4.67
2.88
1.25
1.05
1.01
10.
890.
841
1.23
Orf
,h
ypot
het
ical
prot
ein
yafP
a2.
622
1.13
2.29
3.29
3.18
2.65
1.83
0.84
1.18
1.05
10.
970.
870.
80.
830.
83O
rf,
hyp
oth
etic
alpr
otei
nyd
iYa
2.19
71.
539
4.65
2.39
1.85
2.1
1.37
1.07
1.18
2.86
1.59
1.4
1.28
1.18
1.02
1.14
Orf
,h
ypot
het
ical
prot
ein
ydjM
a2.
629
1.10
41.
923.
083.
032.
651.
941.
030.
891.
031.
010.
850.
81
0.84
0.86
Orf
,h
ypot
het
ical
prot
ein
yebC
1.94
41.
692.
672.
142.
171.
91.
280.
971.
121.
511.
921.
642.
332.
361.
21.
11O
rf,
hyp
oth
etic
alpr
otei
nyf
gB2.
064
1.55
52.
051.
291.
081.
331.
060.
60.
721.
561.
411.
381.
441.
480.
960.
91O
rf,
hyp
oth
etic
alpr
otei
nyg
jO1.
796
1.70
31.
141.
10.
711.
060.
930.
580.
522.
111.
481.
621.
591.
631.
010.
97Pu
tati
veen
zym
eye
bEa
2.37
91.
047
1.56
1.68
1.69
1.49
1.61
0.63
0.72
0.95
0.88
0.71
0.76
0.86
0.88
0.71
Orf
,h
ypot
het
ical
prot
ein
ydgN
1.93
11.
454
1.95
1.05
0.96
0.99
1.23
0.54
0.74
1.85
1.35
1.31
1.26
1.21
0.95
0.97
Puta
tive
mem
bran
epr
otei
nyl
iG1.
774
1.54
42.
141.
761.
32.
281.
31.
010.
972
1.58
1.7
1.95
1.84
1.16
1.19
Orf
,h
ypot
het
ical
prot
ein
ybiN
a2.
072
1.22
22.
92
1.72
2.8
2.13
1.15
1.08
1.31
1.16
1.1
1.3
1.24
1.02
0.98
Orf
,h
ypot
het
ical
prot
ein
dcrB
1.73
21.
498
1.98
1.94
1.51
2.4
2.65
1.21
1.21
1.74
1.48
1.71
2.33
2.18
1.14
1.38
Orf
,h
ypot
het
ical
prot
ein
(con
tinue
d)
59E. coli Gene Expression Profiles After UV
TA
BL
E2
(Con
tinu
ed)
Wild
type
:m
inut
espo
stir
radi
atio
nc
lexA
1:m
inut
espo
stir
radi
atio
n
2060
2060
WT
lexA
1N
o(N
o(N
o(N
oG
ene
(ave
)b(a
ve)
510
2040
60U
V)
UV
)5
1020
4060
UV
)U
V)
Poss
ible
fun
ctio
n
Un
know
ns
(con
tinue
d)yc
ePa
2.02
81.
183
1.79
2.21
1.93
1.44
1.45
0.87
0.87
10.
921.
030.
960.
940.
80.
84O
rf,
hyp
oth
etic
alpr
otei
nyc
iH1.
971
1.22
12.
331.
961.
412.
081.
630.
91.
011.
631.
341.
221.
251.
461.
011.
25O
rf,
hyp
oth
etic
alpr
otei
nye
dM1.
826
1.35
51.
863.
914.
612.
731.
731.
811.
441.
020.
982.
111.
20.
890.
950.
88O
rf,
hyp
oth
etic
alpr
otei
nyc
gW1.
582
ND
1.83
3.12
2.99
3.77
4.47
1.97
2.12
Orf
,h
ypot
het
ical
prot
ein
yebU
1.64
11.
476
4.46
2.75
2.53
3.35
2.21
1.97
1.76
1.74
1.33
1.48
1.5
1.44
1.11
0.92
Puta
tive
nuc
leol
arpr
otei
ns
ycfB
1.75
71.
358
1.89
1.42
0.96
1.68
1.43
0.99
0.69
1.43
1.2
1.26
1.43
1.37
0.88
1.09
Orf
,h
ypot
het
ical
prot
ein
yjiW
a2.
255
0.85
52.
492
1.8
1.71
1.47
0.7
0.98
0.97
1.02
0.98
1.07
0.81
1.15
1.12
Orf
,h
ypot
het
ical
prot
ein
yifL
a2.
185
0.90
71.
551.
431.
631.
651.
170.
680.
930.
90.
710.
90.
640.
870.
93O
rf,
hyp
oth
etic
alpr
otei
nyb
fE1.
677
1.36
42.
462.
52.
913.
422.
041.
271.
911.
241.
081.
141.
51.
350.
860.
99O
rf,
hyp
oth
etic
alpr
otei
nyh
bC1.
276
1.75
41.
780.
991.
090.
770.
760.
820.
871.
411.
061
0.95
0.93
0.62
0.6
Orf
,h
ypot
het
ical
prot
ein
ydeT
a2.
083
0.96
3.17
2.8
1.91
2.47
1.26
1.2
1.03
1.35
1.08
1.05
0.96
1.01
1.17
1.1
Puta
tive
oute
rm
embr
ane
prot
ein
ygcM
1.78
1.25
2.27
1.93
2.22
2.91
1.66
1.33
1.14
1.12
1.2
1.08
1.09
1.26
0.84
1Pu
tati
ve6-
pyru
voyl
tetr
ahyd
robi
opte
rin
syn
thas
eyf
jA1.
548
1.46
72.
711.
481.
321.
951.
481
1.31
1.43
1.48
1.57
1.6
1.88
1.09
1.08
Orf
,h
ypot
het
ical
prot
ein
ychF
1.61
31.
394
2.34
1.96
1.53
2.07
1.7
1.1
1.28
1.84
1.77
1.85
1.87
1.87
1.27
1.37
Puta
tive
GT
P-bi
ndi
ng
prot
ein
ygiR
1.51
31.
494
1.5
0.89
0.77
0.92
1.14
0.55
0.83
1.91
1.44
1.42
1.53
1.32
1.05
0.99
Orf
,h
ypot
het
ical
prot
ein
IS5K
1.69
61.
292
1.82
1.44
1.52
1.75
1.23
0.93
0.9
1.05
1.18
1.07
1.15
1.04
0.83
0.87
Orf
,h
ypot
het
ical
prot
ein
yfhE
1.15
71.
828
0.47
0.57
0.47
0.61
0.57
0.42
0.51
1.34
1.8
1.84
1.63
1.66
0.9
0.91
Orf
,h
ypot
het
ical
prot
ein
yeeA
1.75
31.
229
2.78
2.71
2.63
2.53
1.84
1.47
1.38
1.04
1.14
1.02
0.99
0.85
0.87
0.77
Orf
,h
ypot
het
ical
prot
ein
yaeS
1.67
91.
221
1.68
1.15
1.11
1.4
10.
880.
631.
221.
261.
221.
281.
281.
060.
99O
rf,
hyp
oth
etic
alpr
otei
nya
aH1.
706
1.19
31.
530.
950.
840.
90.
770.
460.
711.
11.
151.
080.
90.
990.
930.
82O
rf,
hyp
oth
etic
alpr
otei
nyc
fQ1.
675
1.28
53.
393.
333.
433.
031.
981.
891.
731.
481.
321.
451.
531.
481.
340.
92O
rf,
hyp
oth
etic
alpr
otei
nb1
228
1.62
41.
330.
610.
860.
981.
371.
010.
560.
631.
231.
151.
171.
271.
30.
890.
95O
rf,
hyp
oth
etic
alpr
otei
nyd
jRa
1.88
41.
055
1.76
2.17
1.58
1.68
1.71
0.85
1.04
1.03
0.84
0.94
0.91
0.92
0.95
0.81
Orf
,h
ypot
het
ical
prot
ein
yrfH
1.48
11.
453
1.24
1.29
0.93
1.66
1.88
10.
891.
181.
231.
41.
61.
61.
010.
92O
rf,
hyp
oth
etic
alpr
otei
nyb
jF1.
627
1.33
81.
71.
311.
311.
731.
270.
810.
991.
681.
461.
61.
51.
621.
181.
17Pu
tati
veen
zym
eya
cL1.
496
1.38
52.
792.
662.
312.
692.
341.
721.
71.
411.
411.
481.
612.
021.
131.
16O
rf,
hyp
oth
etic
alpr
otei
nyf
gK1.
395
1.49
91.
10.
990.
981.
121.
180.
740.
81.
131.
331.
471.
51.
690.
910.
99Pu
tati
veG
TP-
bin
din
gfa
ctor
ydgO
1.44
91.
415
1.67
1.28
1.14
1.04
0.74
0.74
0.88
1.53
1.17
1.17
1.08
1.03
0.88
0.81
Orf
,h
ypot
het
ical
prot
ein
yleA
1.51
21.
345
1.45
1.19
1.01
1.21
0.96
0.66
0.88
1.18
1.45
1.02
1.13
1.24
0.89
0.9
Orf
,h
ypot
het
ical
prot
ein
yiaD
1.53
21.
318
1.95
1.3
1.98
1.61
1.47
0.88
1.29
1.21
1.45
1.74
1.65
1.33
1.1
1.14
Puta
tive
oute
rm
embr
ane
prot
ein
ygeQ
1.42
41.
423
2.43
1.57
1.73
1.54
1.24
1.3
1.09
1.18
1.06
1.15
1.09
1.21
0.74
0.86
Orf
,h
ypot
het
ical
prot
ein
yccF
a1.
765
1.06
72.
051.
71.
843.
041.
341.
041.
221.
40.
861.
091.
181.
020.
981.
1O
rf,
hyp
oth
etic
alpr
otei
nya
bO1.
624
1.20
71.
191.
11.
151.
10.
820.
610.
711.
091.
11.
011.
011.
10.
870.
89O
rf,
hyp
oth
etic
alpr
otei
nyh
dJ1.
686
1.11
72.
551.
711.
231.
380.
760.
731.
081.
551.
071.
161.
031.
110.
951.
17Pu
tati
vem
eth
yltr
ansf
eras
e
aIn
duce
din
ale
xA-d
epen
den
tm
ann
er.
bA
vere
pres
ents
the
aver
age
tran
scri
ptle
vel
inir
radi
ated
sam
ples
com
pare
dto
that
inun
irra
diat
edsa
mpl
esas
desc
ribe
din
mat
eria
lsan
dm
eth
od
s.cV
alue
sre
pres
ent
the
fold
chan
gein
tran
scri
ptle
vel
atth
eti
me
indi
cate
dco
mpa
red
toth
ebe
gin
nin
gof
the
expe
rim
ent
asde
scri
bed
inm
ater
ials
and
met
ho
ds.
60 J. Courcelle et al.
Figure 5.—Representation of genes that displayed a reduced level of transcripts following UV irradiation. The change intranscript levels for the indicated gene is plotted as in Figure 2. (A) A typical operon in which the transcript from both wild-type cells and lexA1 mutants was observed to be reduced. (B) An operon in which the transcript from wild-type cells was observedto be severely reduced at the 59 end. (C) Three operons in which transcripts were reduced in wild-type cells throughout theoperon.
transcription or degradation of transcripts occurs in a gat operon, the decrease in transcript levels followingUV irradiation was observed in both wild-type and lexA1lexA-dependent manner, and it may point to a lexA-
dependent mechanism for inhibition of transcription cells (Figure 5A). In the wild-type cells, the time at whichtranscripts recovered to preirradiation levels varied butor enhanced degradation of these transcripts. Due to
the small sample size of this experiment, we are inclined generally occurred prior to 40 min postirradiation. In-terestingly, whereas transcripts recovered to pretreat-to interpret these findings cautiously. However, further
investigation of these observations is clearly warranted. ment levels in the wild-type cells, transcripts of severalgenes failed to recover in lexA1 mutants within the pe-The phenomenon of downregulation is also interest-
ing to consider with respect to DNA repair. Actively riod observed in these experiments, suggesting that lexA-regulated genes have an important role in this transcrip-transcribed genes in E.coli are repaired preferentially
compared to nontranscribed genes (Mellon and Hana- tional recovery (Figure 5A).The gat operon, controlling galactitol uptake and me-walt 1989). When the lac operon is actively transcribed
at the time of UV irradiation, repair of the transcribed tabolism, is one of several operons involved in the me-tabolism of different carbon sources, which were foundstrand occurs within 5 min after irradiation. While it is
assumed that this response allows for the rapid transcrip- to have reduced transcript levels following UV irradia-tion. Other carbon metabolism operons whose tran-tional recovery of expressed genes, little is known about
the actual inhibition or recovery of transcription for script levels decreased include fru, man, wwb, glg, andmal . Our cultures were grown with glucose as the soleoperons other than lac in E. coli.
Diminished transcript levels were clearly evident in carbon source. It may be interesting to know how thesemetabolic pathways are regulated when cells are grownsome operons. Several different temporal profiles were
observed (Figure 5). In some cases, exemplified by the in the presence of their respective carbon sources.
61E. coli Gene Expression Profiles After UV
TA
BL
E3
Ope
rons
wit
hre
duce
dtr
ansc
ript
leve
lsfo
llow
ing
UV
-irra
diat
ion
Wild
type
:m
inut
espo
stir
radi
atio
nb
lexA
1:m
inut
espo
stir
radi
atio
nL
ocat
ion
inkb
and
2060
2060
stra
nd
WT
lexA
1(N
o(N
o(N
o(N
oO
pero
ntr
ansc
ribe
d(a
ve)a
(ave
)5
1020
4060
UV
)U
V)
510
2040
60U
V)
UV
)Po
ssib
lefu
nct
ion
araD
652
0.85
1.07
0.82
1.08
0.98
1.33
1.4
1.12
1.51
1.04
1.06
1.01
1.07
1.15
11
l-ri
bulo
se-5
-ph
osph
ate
4-ep
imer
ase
araA
0.58
ND
0.48
0.38
0.84
0.79
0.93
1.22
0.93
1.08
0.98
0.99
0.96
l-ar
abin
ose
isom
eras
ear
aB0.
651.
050.
630.
710.
241.
041.
161.
141.
190.
971.
051
1.05
1.13
10.
99l-
ribu
loki
nas
e
mod
F79
120.
670.
450.
440.
540.
541.
371.
91.
191.
680.
40.
680.
730.
680.
441.
3A
TP-
bin
din
gco
mpo
nen
tof
mol
ybda
tetr
ansp
ort
syst
em
ybiC
8351
0.62
0.51
1.28
1.01
1.04
0.93
0.93
1.48
1.86
0.85
0.9
0.89
0.84
0.57
1.57
1.61
Puta
tive
deh
ydro
gen
ase
ybiK
8651
0.83
0.93
0.74
0.84
11.
522.
221.
441.
590.
491.
061.
381.
421.
131.
21.
15Pu
tati
veas
para
gin
ase
yliA
0.63
0.73
0.35
0.42
0.54
0.8
1.22
0.79
1.32
0.57
0.76
0.76
0.71
0.63
0.92
0.95
Puta
tive
AT
P-bi
ndi
ng
com
pon
ent
ofa
tran
spor
tsy
stem
yliA
ND
0.79
1.01
0.7
0.79
0.68
0.59
1.04
0.86
Puta
tive
AT
P-bi
ndi
ng
com
pon
ent
ofa
tran
spor
tsy
stem
yliB
0.62
0.56
0.36
0.36
0.43
0.65
0.88
0.85
0.89
0.3
0.46
0.7
0.59
0.46
0.95
0.83
Puta
tive
tran
spor
tpr
otei
nyl
iC0.
60.
830.
470.
340.
420.
550.
790.
80.
910.
710.
850.
850.
820.
710.
930.
97Pu
tati
vetr
ansp
ort
syst
empe
rmea
sepr
otei
nyl
iD0.
740.
610.
580.
320.
440.
630.
780.
850.
630.
460.
490.
650.
610.
520.
890.
89Pu
tati
vetr
ansp
ort
syst
empe
rmea
sepr
otei
n
min
C12
232
0.33
0.65
1.31
0.73
0.52
0.64
0.96
2.45
2.61
0.79
0.94
0.83
0.82
0.58
1.2
1.23
Cel
ldi
visi
onin
hib
itor
,in
hib
its
ftsZ
rin
gfo
rmat
ion
min
D0.
450.
631.
520.
810.
60.
740.
782.
11.
840.
80.
930.
880.
720.
541.
371.
1C
ell
divi
sion
inh
ibit
or,
am
embr
ane
AT
Pase
,ac
tiva
tes
min
Cm
inE
0.33
0.94
1.03
0.59
0.46
0.58
0.64
1.87
2.17
0.96
0.98
1.02
1.1
0.84
1.05
1.03
Cel
ldi
visi
onto
polo
gica
lsp
ecifi
city
fact
or
treA
1244
20.
480.
72.
291.
151.
271
1.09
32.
70.
990.
890.
880.
80.
841.
271.
25T
reh
alas
e,pe
ripl
asm
ic
ycgC
1246
20.
490.
540.
650.
650.
710.
881.
231.
391.
960.
540.
590.
580.
560.
40.
990.
99Pu
tati
vePT
Ssy
stem
enzy
me
Iyc
gS0.
690.
670.
770.
520.
350.
580.
880.
880.
920.
770.
740.
720.
70.
671.
121.
04Pu
tati
vedi
hyd
roxy
acet
one
kin
ase
ycgT
0.8
ND
0.99
0.59
0.62
0.77
1.01
0.86
1.12
0.95
0.94
1.1
Puta
tive
dih
ydro
xyac
eton
eki
nas
eyc
gTN
D0.
780.
810.
81.
140.
790.
71.
121.
06Pu
tati
vedi
hyd
roxy
acet
one
kin
ase
ydcL
1500
10.
590.
571.
971.
231.
430.
90.
772.
192.
050.
90.
850.
720.
430.
311.
30.
96O
rf,
hyp
oth
etic
alpr
otei
n
yddU
1561
2N
DN
D0.
680.
790.
740.
841.
09Pu
tati
veen
zym
eyd
dV0.
270.
790.
710.
570.
730.
560.
732.
292.
610.
850.
970.
920.
730.
881.
071.
14O
rf,
hyp
oth
etic
alpr
otei
n
pqqL
1570
2N
D0.
710.
720.
790.
770.
910.
881.
241.
05Pu
tati
vepe
ptid
ase
yddB
0.38
0.66
0.93
0.6
0.64
1.18
1.25
2.25
2.54
0.68
0.83
0.84
1.19
1.01
1.7
1.05
Orf
,h
ypot
het
ical
prot
ein
yddA
0.6
0.87
0.73
0.5
0.84
1.2
1.19
1.3
1.67
0.96
1.1
1.08
1.21
1.14
1.3
1.22
Puta
tive
AT
P-bi
ndi
ng
com
pon
ent
ofa
tran
spor
tsy
stem
yeaG
1864
10.
50.
631.
411.
321.
461.
10.
962.
862.
180.
880.
931.
070.
720.
581.
491.
16O
rf,
hyt
poth
etic
alpr
otei
nye
aH18
661
0.5
0.62
0.61
0.62
0.95
0.58
0.52
1.2
1.44
0.69
0.95
0.84
0.65
0.58
1.21
1.18
Orf
,h
ypot
het
ical
prot
ein
man
X19
001
0.58
0.44
1.16
0.51
0.39
0.54
0.75
1.01
1.31
0.71
0.67
0.46
0.38
0.3
1.28
1.02
PTS
enzy
me
IIA
B,
man
nos
e-sp
ecifi
cm
anY
0.55
0.55
1.18
0.72
0.33
0.61
0.74
1.3
1.31
0.82
0.64
0.53
0.48
0.42
1.07
1.04
PTS
enzy
me
IIC
,m
ann
ose-
spec
ific
man
Z0.
730.
61.
230.
650.
480.
550.
70.
921.
050.
820.
740.
570.
490.
421.
060.
96PT
Sen
zym
eII
D,
man
nos
e-sp
ecifi
c
(con
tinue
d)
62 J. Courcelle et al.
TA
BL
E3
(Con
tinu
ed)
Wild
type
:m
inut
espo
stir
radi
atio
nb
lexA
1:m
inut
espo
stir
radi
atio
nL
ocat
ion
inkb
and
2060
2060
stra
nd
WT
lexA
1(N
o(N
o(N
o(N
oO
pero
ntr
ansc
ribe
d(a
ve)b
(ave
)5
1020
4060
UV
)U
V)
510
2040
60U
V)
UV
)Po
ssib
lefu
nct
ion
IS5I
2099
20.
981.
161.
070.
70.
560.
760.
760.
561.
011.
151.
11.
171.
311.
281.
011.
06IS
5tr
ansp
osas
ew
bbL
0.49
0.89
0.61
0.25
0.41
1.12
1.25
1.27
1.7
0.73
0.77
0.76
0.86
0.96
0.92
0.91
Puta
tive
crea
tin
ase
wbb
K0.
470.
660.
490.
240.
391.
31.
61.
531.
910.
270.
260.
290.
450.
830.
690.
58Pu
tati
vegl
ucos
etr
ansf
eras
ew
bbJ
0.55
0.74
0.77
0.53
0.79
1.41
1.65
1.64
2.12
0.48
0.54
0.56
0.71
0.71
0.79
0.83
Puta
tive
o-a
cety
ltr
ansf
eras
ew
bbI
0.41
0.93
0.52
0.5
0.9
1.37
1.31
22.
460.
610.
690.
790.
870.
930.
870.
8Pu
tati
veG
alf
tran
sfer
ase
rfc
0.53
1.14
0.37
0.3
0.59
1.05
0.95
1.14
1.3
0.6
0.59
0.71
0.75
1.04
0.68
0.61
o-A
nti
gen
poly
mer
ase
glf
ND
0.88
0.62
0.64
0.62
0.7
0.88
0.79
0.78
UD
P-ga
lact
opyr
anos
em
utas
e
gatR
_220
692
0.76
0.9
1.33
0.8
0.71
0.94
0.8
1.15
1.26
0.96
0.9
0.93
0.92
0.86
0.95
1.07
Split
gala
ctit
olut
iliza
tion
oper
onre
pres
sor,
frag
men
t2
gatD
0.36
0.43
1.05
0.22
0.16
0.28
0.67
1.18
1.46
0.41
0.35
0.33
0.35
0.36
0.89
0.77
Gal
acti
tol-1
-ph
osph
ate
deh
ydro
gen
ase
gatC
0.41
0.33
1.22
0.51
0.29
0.43
0.66
1.71
1.3
0.6
0.39
0.25
0.24
0.17
1.05
0.95
PTS
syst
emga
lact
itol
-spe
cifi
cen
zym
eII
Cga
tB0.
450.
351.
480.
460.
250.
410.
871.
471.
60.
570.
320.
270.
250.
220.
970.
88G
alac
tito
l-spe
cifi
cen
zym
eII
Bph
osph
otra
nsf
eras
esy
stem
gatA
0.34
0.35
1.1
0.37
0.16
0.43
0.73
1.61
1.71
0.49
0.39
0.31
0.27
0.24
10.
93G
alac
tito
l-spe
cifi
cen
zym
eII
Aph
osph
otra
nsf
eras
esy
stem
gatZ
0.51
0.28
0.98
0.39
0.25
0.54
0.93
1.29
1.14
0.42
0.3
0.25
0.22
0.14
10.
89Pu
tati
veta
gato
se6-
phos
phat
eki
nas
e1
gatY
0.46
0.32
0.82
0.46
0.45
0.6
11.
551.
320.
450.
410.
360.
310.
211.
111.
08T
agat
ose-
bisp
hos
phat
eal
dola
se1
fruA
2260
20.
60.
90.
320.
420.
410.
440.
660.
720.
770.
890.
940.
880.
930.
940.
961.
07PT
Ssy
stem
,fr
ucto
se-s
peci
fic
tran
spor
tpr
otei
nfr
uK0.
570.
580.
40.
320.
230.
410.
790.
830.
680.
870.
610.
640.
620.
731.
311.
07Fr
ucto
se-1
-ph
osph
ate
kin
ase
fruB
0.4
0.73
0.27
0.2
0.11
0.37
0.9
10.
860.
840.
531.
570.
710.
71.
131.
26PT
Ssy
stem
,fr
ucto
se-s
peci
fic
IIA
/fpr
com
pon
ent
yfbE
2363
10.
490.
531.
661.
170.
850.
880.
972.
911.
610.
850.
790.
850.
80.
81.
441.
62Pu
tati
veen
zym
e
mal
P35
452
0.5
0.67
0.97
0.71
0.75
0.61
1.04
1.73
1.55
0.76
0.72
0.92
0.78
0.64
1.28
1.01
Mal
tode
xtri
nph
osph
oryl
ase
mal
Q0.
560.
840.
690.
320.
560.
390.
470.
870.
870.
980.
931.
020.
950.
791.
191.
044-
a-g
luca
not
ran
sfer
ase
(am
ylom
alta
se)
glpD
3560
10.
56N
D0.
220.
370.
40.
30.
610.
660.
69sn
-gly
cero
l-3-p
hos
phat
ede
hyd
roge
nas
e(a
erob
ic)
glgP
3561
20.
620.
550.
490.
30.
50.
510.
660.
680.
90.
440.
50.
740.
680.
641.
151.
04G
lyco
gen
phos
phor
ylas
egl
gA0.
390.
590.
30.
260.
430.
370.
490.
741.
160.
460.
50.
750.
790.
661.
11.
06G
lyco
gen
syn
thas
egl
gC0.
630.
630.
570.
530.
50.
640.
871.
010.
960.
50.
660.
80.
790.
621.
051.
1G
lyco
se-1
-ph
osph
ate
aden
ylyl
tran
sfer
ase
glgX
0.64
0.54
0.33
0.48
0.5
0.61
0.86
0.94
0.81
0.36
0.49
0.68
0.57
0.47
0.99
0.91
Agl
ycos
yll
hyd
rola
se,
debr
anch
ing
enzy
me
glgB
0.71
0.62
0.72
0.67
0.45
0.8
0.99
0.94
1.11
0.56
0.72
0.84
0.7
0.64
1.17
1.05
1,4-
a-g
luca
nbr
anch
ing
enzy
me
nlpA
3836
20.
610.
431.
471.
111.
051.
92.
42.
62.
620.
490.
620.
620.
520.
461.
251.
3L
ipop
rote
in-2
8
aceB
4213
10.
670.
551.
481.
230.
781.
241.
952.
371.
610.
770.
790.
710.
550.
431.
351.
02M
alat
esy
nth
ase
Aac
eA1
0.64
1.82
0.56
0.57
0.49
0.97
0.81
0.96
0.74
0.67
0.58
0.53
0.35
1.01
0.77
Isoc
itra
tely
ase
aceK
0.46
0.44
0.59
0.46
0.37
0.38
0.79
1.14
1.11
0.42
0.44
0.36
0.3
0.24
0.9
0.71
Isoc
itra
tede
hyd
roge
nas
eki
nas
e/ph
osph
atas
e
aA
vere
pres
ents
the
aver
age
tran
scri
ptle
vel
inir
radi
ated
sam
ples
com
pare
dto
that
inun
irra
diat
edsa
mpl
esas
desc
ribe
din
mat
eria
lsan
dm
eth
od
s.bV
alue
sre
pres
ent
the
fold
chan
gein
tran
scri
ptle
vel
atth
eti
me
indi
cate
dco
mpa
red
toth
ebe
gin
nin
gof
the
expe
rim
ent
asde
scri
bed
inm
ater
ials
and
met
ho
ds.
63E. coli Gene Expression Profiles After UV
supported by the National Institutes of Health (NIH), MolecularA second form of repression profile is exemplified byBiophysics training grant GM08295-11. The work was supported bythe rfa operon, which encodes gene products involvedNIH grants to Nicholas R. Cozzarelli and David Botstein. P.O.B. was
in lipid synthesis in the membrane. The rfa operon supported by the Howard Hughes Medical Institute and NIH grantdisplayed a loss of transcript following UV irradiation HG00983. P.O.B. is an associate investigator at the Howard Hughes
Medical Institute. Research by P.C.H. is supported by an Outstandingin wild-type cells, but not in the lexA1 mutant. The lossInvestigator grant CA44349 from the National Cancer Institute.of transcript was more severe at the 59 end of the operon,
which may at least partially reflect the fact that mostRNA degradation in E. coli is believed to occur 39–59(Figure 5B). LITERATURE CITED
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