Genetics, Vol. 158, 41-64, May 2001, Copyright © 2001

Comparative Gene Expression Profiles Following UV Exposure in Wild-Type and SOS-Deficient Escherichia coli

Justin Courcellec, Arkady Khodurskya, Brian Peterb, Patrick O. Browna, and Philip C. Hanawaltd
a Department of Biochemistry, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305,
b Department of MCB, UC-Berkeley, Berkeley, California 94720,
c Department of Biological Science, Mississippi State University, Mississippi State, Mississippi 39762
d Department of Biological Sciences, Stanford University, Stanford, California 94305

Corresponding author: Justin Courcelle, Department of Biological Science, P.O. Box GY, Mississippi State University, Mississippi State, MS 39762., jcourcelle{at}biology.msstate.edu (E-mail)

Communicating editor: P. L. FOSTER

The 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 DNA fragments from 95.5% of all open reading frames identified on the E. coli chromosome, we have examined the changes in gene expression following UV exposure in both wild-type cells and lexA1 mutants, which are unable to induce genes under LexA control. We report here the time courses of expression of the genes surrounding the 26 documented lexA-regulated regions on the E. coli chromosome. We observed 17 additional sites that responded in a lexA-dependent manner and a large number of genes that were upregulated in a lexA-independent manner although upregulation in this manner was generally not more than twofold. In addition, several transcripts were either downregulated or degraded following UV irradiation. These newly identified UV-responsive genes are discussed with respect to their possible roles in cellular recovery following exposure to UV irradiation.




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M. Jara, C. Nunuz, S. Campoy, A. R. Fernandez de Henestrosa, D. R. Lovley, and J. Barbe
Geobacter sulfurreducens Has Two Autoregulated lexA Genes Whose Products Do Not Bind the recA Promoter: Differing Responses of lexA and recA to DNA Damage
J. Bacteriol., April 15, 2003; 185(8): 2493 - 2502.
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 Proc. Natl. Acad. Sci. USAHome page
A. Lobner-Olesen, M. G. Marinus, and F. G. Hansen
Role of SeqA and Dam in Escherichia coli gene expression: A global/microarray analysis
PNAS, April 15, 2003; 100(8): 4672 - 4677.
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 Proc. Natl. Acad. Sci. USAHome page
Y. Liu, J. Zhou, M. V. Omelchenko, A. S. Beliaev, A. Venkateswaran, J. Stair, L. Wu, D. K. Thompson, D. Xu, I. B. Rogozin, et al.
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
PNAS, April 1, 2003; 100(7): 4191 - 4196.
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 J. Biol. Chem.Home page
E. A. Stohl, J. P. Brockman, K. L. Burkle, K. Morimatsu, S. C. Kowalczykowski, and H. S. Seifert
Escherichia coli RecX Inhibits RecA Recombinase and Coprotease Activities in Vitro and in Vivo
J. Biol. Chem., January 17, 2003; 278(4): 2278 - 2285.
[Abstract] [Full Text] [PDF]

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 J. Bacteriol.Home page
A. R. Fernandez de Henestrosa, J. Cune, I. Erill, J. K. Magnuson, and J. Barbe
A Green Nonsulfur Bacterium, Dehalococcoides ethenogenes, with the LexA Binding Sequence Found in Gram-Positive Organisms
J. Bacteriol., November 1, 2002; 184(21): 6073 - 6080.
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 MicrobiologyHome page
S. Campoy, G. Mazon, A. R. Fernandez de Henestrosa, M. Llagostera, P. B. Monteiro, and J. Barbe
A new regulatory DNA motif of the gamma subclass Proteobacteria: identification of the LexA protein binding site of the plant pathogen Xylella fastidiosa
Microbiology, November 1, 2002; 148(11): 3583 - 3597.
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 MicrobiologyHome page
E. M. Dullaghan, P. C. Brooks, and E. O. Davis
The role of multiple SOS boxes upstream of the Mycobacterium tuberculosis lexA gene - identification of a novel DNA-damage-inducible gene
Microbiology, November 1, 2002; 148(11): 3609 - 3615.
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 J. Biol. Chem.Home page
C. J. Kluck, H. Patzelt, P. Genevaux, D. Brehmer, W. Rist, J. Schneider-Mergener, B. Bukau, and M. P. Mayer
Structure-Function Analysis of HscC, the Escherichia coli Member of a Novel Subfamily of Specialized Hsp70 Chaperones
J. Biol. Chem., October 18, 2002; 277(43): 41060 - 41069.
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 Nucleic Acids ResHome page
J. Lin, J. Qian, D. Greenbaum, P. Bertone, R. Das, N. Echols, A. Senes, B. Stenger, and M. Gerstein
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing
Nucleic Acids Res., October 15, 2002; 30(20): 4574 - 4582.
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 J. Biol. Chem.Home page
S. Kobayashi, M. R. Valentine, P. Pham, M. O'Donnell, and M. F. Goodman
Fidelity of Escherichia coli DNA Polymerase IV. PREFERENTIAL GENERATION OF SMALL DELETION MUTATIONS BY dNTP-STABILIZED MISALIGNMENT
J. Biol. Chem., September 6, 2002; 277(37): 34198 - 34207.
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 Proc. Natl. Acad. Sci. USAHome page
H. Li, V. Rhodius, C. Gross, and E. D. Siggia
Identification of the binding sites of regulatory proteins in bacterial genomes
PNAS, September 3, 2002; 99(18): 11772 - 11777.
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 Proc. Natl. Acad. Sci. USAHome page
P. Pham, E. M. Seitz, S. Saveliev, X. Shen, R. Woodgate, M. M. Cox, and M. F. Goodman
Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis
PNAS, August 20, 2002; 99(17): 11061 - 11066.
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 Proc. Natl. Acad. Sci. USAHome page
M. Ronen, R. Rosenberg, B. I. Shraiman, and U. Alon
Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
PNAS, August 6, 2002; 99(16): 10555 - 10560.
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 Nucleic Acids ResHome page
C. Sabatti, L. Rohlin, M.-K. Oh, and J. C. Liao
Co-expression pattern from DNA microarray experiments as a tool for operon prediction
Nucleic Acids Res., July 1, 2002; 30(13): 2886 - 2893.
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 J. Bacteriol.Home page
A. Borden, P. I. O'Grady, D. Vandewiele, A. R. Fernandez de Henestrosa, C. W. Lawrence, and R. Woodgate
Escherichia coli DNA Polymerase III Can Replicate Efficiently past a T-T cis-syn Cyclobutane Dimer if DNA Polymerase V and the 3' to 5' Exonuclease Proofreading Function Encoded by dnaQ Are Inactivated
J. Bacteriol., May 15, 2002; 184(10): 2674 - 2681.
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 Proc. Natl. Acad. Sci. USAHome page
M. D. Sutton, I. Narumi, and G. C. Walker
Posttranslational modification of the umuD-encoded subunit of Escherichia coli DNA polymerase V regulates its interactions with the beta processivity clamp
PNAS, April 16, 2002; 99(8): 5307 - 5312.
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 Nucleic Acids ResHome page
A. Tapias, S. Fernandez, J. C. Alonso, and J. Barbe
Rhodobacter sphaeroides LexA has dual activity: optimising and repressing recA gene transcription
Nucleic Acids Res., April 1, 2002; 30(7): 1539 - 1546.
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 Proc. Natl. Acad. Sci. USAHome page
B. Van Houten, J. A. Eisen, and P. C. Hanawalt
A cut above: Discovery of an alternative excision repair pathway in bacteria
PNAS, March 5, 2002; 99(5): 2581 - 2583.
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 J. Bacteriol.Home page
B. T. Smith, A. D. Grossman, and G. C. Walker
Localization of UvrA and Effect of DNA Damage on the Chromosome of Bacillus subtilis
J. Bacteriol., January 15, 2002; 184(2): 488 - 493.
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 GeneticsHome page
Y. Nagata, K. Mashimo, M. Kawata, and K. Yamamoto
The Roles of Klenow Processing and Flap Processing Activities of DNA Polymerase I in Chromosome Instability in Escherichia coli K12 Strains
Genetics, January 1, 2002; 160(1): 13 - 23.
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 J. Bacteriol.Home page
K. LeVier and G. C. Walker
Genetic Analysis of the Sinorhizobium meliloti BacA Protein: Differential Effects of Mutations on Phenotypes
J. Bacteriol., November 1, 2001; 183(21): 6444 - 6453.
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