Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays

Jochmann N, Kurze A-K, Czaja LF, Brinkrolf K, Brune I, Hueser AT, Hansmeier N, Pühler A, Borovok I, Tauch A (2009)
MICROBIOLOGY 155(5): 1459-1477.

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The lexA gene of Corynebacterium glutamicum ATCC 13032 was deleted to create the mutant strain C. glutamicum NJ2114, which has an elongated cell morphology and an increased doubling time. To characterize the SOS regulon in C. glutamicum, the transcriptomes of NJ2114 and a DNA-damage-induced wild-type strain were compared with that of a wild-type control using DNA microarray hybridization. The expression data were combined with bioinformatic pattern searches for LexA binding sites, leading to the detection of 46 potential SOS boxes located upstream of differentially expressed transcription units. Binding of a hexahistidyl-tagged LexA protein to 40 double-stranded oligonucleotides containing the potential SOS boxes was demonstrated in vitro by DNA band shift assays. It turned out that LexA binds not only to SOS boxes in the promoter-operator region of upregulated genes, but also to SOS boxes detected upstream of downregulated genes. These results demonstrated that LexA controls directly the expression of at least 48 SOS genes organized in 36 transcription units. The deduced genes encode a variety of physiological functions, many of them involved in DNA repair and survival after DNA damage, but nearly half of them have hitherto unknown functions. Alignment of the LexA binding sites allowed the corynebacterial SOS box consensus sequence TcGAA(a/c)AnnTGTtCGA to be deduced. Furthermore, the common intergenic region of lexA and the differentially expressed divS-nrdR operon, encoding a cell division suppressor and a regulator of deoxyribonucleotide biosynthesis, was characterized in detail. Promoter mapping revealed differences in divS-nrdR expression during SOS response and normal growth conditions. One of the four LexA binding sites detected in the intergenic region is involved in regulating divS-nrdR transcription, whereas the other sites are apparently used for negative autoregulation of lexA expression.
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MICROBIOLOGY
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155
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5
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1459-1477
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Jochmann N, Kurze A-K, Czaja LF, et al. Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays. MICROBIOLOGY. 2009;155(5):1459-1477.
Jochmann, N., Kurze, A. - K., Czaja, L. F., Brinkrolf, K., Brune, I., Hueser, A. T., Hansmeier, N., et al. (2009). Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays. MICROBIOLOGY, 155(5), 1459-1477. doi:10.1099/mic.0.025841-0
Jochmann, N., Kurze, A. - K., Czaja, L. F., Brinkrolf, K., Brune, I., Hueser, A. T., Hansmeier, N., Pühler, A., Borovok, I., and Tauch, A. (2009). Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays. MICROBIOLOGY 155, 1459-1477.
Jochmann, N., et al., 2009. Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays. MICROBIOLOGY, 155(5), p 1459-1477.
N. Jochmann, et al., “Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays”, MICROBIOLOGY, vol. 155, 2009, pp. 1459-1477.
Jochmann, N., Kurze, A.-K., Czaja, L.F., Brinkrolf, K., Brune, I., Hueser, A.T., Hansmeier, N., Pühler, A., Borovok, I., Tauch, A.: Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays. MICROBIOLOGY. 155, 1459-1477 (2009).
Jochmann, Nina, Kurze, Anna-Katharina, Czaja, Lisa F., Brinkrolf, Karina, Brune, Iris, Hueser, Andrea T., Hansmeier, Nicole, Pühler, Alfred, Borovok, Ilya, and Tauch, Andreas. “Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays”. MICROBIOLOGY 155.5 (2009): 1459-1477.

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PMID: 28484430
The small 6C RNA of Corynebacterium glutamicum is involved in the SOS response.
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PMID: 27362471
Ciprofloxacin triggered glutamate production by Corynebacterium glutamicum.
Lubitz D, Wendisch VF., BMC Microbiol 16(1), 2016
PMID: 27717325
An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria.
Sanchez-Alberola N, Campoy S, Emerson D, Barbé J, Erill I., J Bacteriol 197(16), 2015
PMID: 25986903
Analysis of SOS-induced spontaneous prophage induction in Corynebacterium glutamicum at the single-cell level.
Nanda AM, Heyer A, Krämer C, Grünberger A, Kohlheyer D, Frunzke J., J Bacteriol 196(1), 2014
PMID: 24163339
Cell division in Corynebacterineae.
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PMID: 24782835
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032.
Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A, Rückert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24138339
Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators.
Hödar C, Moreno P, di Genova A, Latorre M, Reyes-Jara A, Maass A, González M, Cambiazo V., Biometals 25(1), 2012
PMID: 21830017
Global analysis of the regulon of the transcriptional repressor LexA, a key component of SOS response in Mycobacterium tuberculosis.
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PMID: 22528497
Inference of self-regulated transcriptional networks by comparative genomics.
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PMID: 23032607
DNA repair and genome maintenance in Bacillus subtilis.
Lenhart JS, Schroeder JW, Walsh BW, Simmons LA., Microbiol Mol Biol Rev 76(3), 2012
PMID: 22933559
The Zur regulon of Corynebacterium glutamicum ATCC 13032.
Schröder J, Jochmann N, Rodionov DA, Tauch A., BMC Genomics 11(), 2010
PMID: 20055984

77 References

Daten bereitgestellt von Europe PubMed Central.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
The ATP-cone: an evolutionarily mobile, ATP-binding regulatory domain.
Aravind L, Wolf YI, Koonin EV., J. Mol. Microbiol. Biotechnol. 2(2), 2000
PMID: 10939243
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593
CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.
Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A., J. Biotechnol. 129(2), 2006
PMID: 17229482
Fast index based algorithms and software for matching position specific scoring matrices.
Beckstette M, Homann R, Giegerich R, Kurtz S., BMC Bioinformatics 7(), 2006
PMID: 16930469
FtsK, a literate chromosome segregation machine.
Bigot S, Sivanathan V, Possoz C, Barre FX, Cornet F., Mol. Microbiol. 64(6), 2007
PMID: 17511809
Alternative oxygen-dependent and oxygen-independent ribonucleotide reductases in Streptomyces: cross-regulation and physiological role in response to oxygen limitation.
Borovok I, Gorovitz B, Yanku M, Schreiber R, Gust B, Chater K, Aharonowitz Y, Cohen G., Mol. Microbiol. 54(4), 2004
PMID: 15522084
Mechanism of action of the lexA gene product.
Brent R, Ptashne M., Proc. Natl. Acad. Sci. U.S.A. 78(7), 1981
PMID: 7027256
The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum.
Brinkrolf K, Brune I, Tauch A., J. Biotechnol. 129(2), 2006
PMID: 17227685
The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum.
Brune I, Jochmann N, Brinkrolf K, Huser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Puhler A, Tauch A., J. Bacteriol. 189(7), 2007
PMID: 17259312
The bacterial LexA transcriptional repressor.
Butala M, Zgur-Bertok D, Busby SJ., Cell. Mol. Life Sci. 66(1), 2009
PMID: 18726173
WebLogo: a sequence logo generator.
Crooks GE, Hon G, Chandonia JM, Brenner SE., Genome Res. 14(6), 2004
PMID: 15173120
Characterization of the SOS regulon of Caulobacter crescentus.
da Rocha RP, Paquola AC, Marques Mdo V, Menck CF, Galhardo RS., J. Bacteriol. 190(4), 2007
PMID: 18083815
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856

Dullaghan, Microbiology (Reading, Engl.) 148(11), 2002
Profile hidden Markov models.
Eddy SR., Bioinformatics 14(9), 1998
PMID: 9918945
Aeons of distress: an evolutionary perspective on the bacterial SOS response.
Erill I, Campoy S, Barbe J., FEMS Microbiol. Rev. 31(6), 2007
PMID: 17883408
Identification of additional genes belonging to the LexA regulon in Escherichia coli.
Fernandez De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R., Mol. Microbiol. 35(6), 2000
PMID: 10760155
The Pfam protein families database.
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18039703
An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus.
Galhardo RS, Rocha RP, Marques MV, Menck CF., Nucleic Acids Res. 33(8), 2005
PMID: 15886391
Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants.
Grant SG, Jessee J, Bloom FR, Hanahan D., Proc. Natl. Acad. Sci. U.S.A. 87(12), 1990
PMID: 2162051
LexA regulates the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803 as a transcription activator.
Gutekunst K, Phunpruch S, Schwarz C, Schuchardt S, Schulz-Friedrich R, Appel J., Mol. Microbiol. 58(3), 2005
PMID: 16238629

AUTHOR UNKNOWN, Gene 77(), 1989
Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source.
Huser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Puhler A, Wiegrabe I, Tauch A., J. Biotechnol. 106(2-3), 2003
PMID: 14651867
A MOLECULAR MECHANISM OF MITOMYCIN ACTION: LINKING OF COMPLEMENTARY DNA STRANDS.
IYER VN, SZYBALSKI W., Proc. Natl. Acad. Sci. U.S.A. 50(), 1963
PMID: 14060656
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
New functions for Y family polymerases.
Lehmann AR., Mol. Cell 24(4), 2006
PMID: 17188030

AUTHOR UNKNOWN, Biochimie 73(), 1991
The SOS regulatory system of Escherichia coli.
Little JW, Mount DW., Cell 29(1), 1982
PMID: 7049397
Purified lexA protein is a repressor of the recA and lexA genes.
Little JW, Mount DW, Yanisch-Perron CR., Proc. Natl. Acad. Sci. U.S.A. 78(7), 1981
PMID: 7027255
Reconstruction of the evolutionary history of the LexA-binding sequence.
Mazon G, Erill I, Campoy S, Cortes P, Forano E, Barbe J., Microbiology (Reading, Engl.) 150(Pt 11), 2004
PMID: 15528664
Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum.
McHardy AC, Tauch A, Ruckert C, Puhler A, Kalinowski J., J. Biotechnol. 104(1-3), 2003
PMID: 12948641
Tapping-mode atomic force microscopy produces faithful high-resolution images of protein surfaces.
Moller C, Allen M, Elings V, Engel A, Muller DJ., Biophys. J. 77(2), 1999
PMID: 10423460
Inhibition of FtsZ polymerization by SulA, an inhibitor of septation in Escherichia coli.
Mukherjee A, Cao C, Lutkenhaus J., Proc. Natl. Acad. Sci. U.S.A. 95(6), 1998
PMID: 9501185
All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis.
Napolitano R, Janel-Bintz R, Wagner J, Fuchs RP., EMBO J. 19(22), 2000
PMID: 11080171
DivS, a novel SOS-inducible cell-division suppressor in Corynebacterium glutamicum.
Ogino H, Teramoto H, Inui M, Yukawa H., Mol. Microbiol. 67(3), 2007
PMID: 18086211
The Y-family of DNA polymerases.
Ohmori H, Friedberg EC, Fuchs RP, Goodman MF, Hanaoka F, Hinkle D, Kunkel TA, Lawrence CW, Livneh Z, Nohmi T, Prakash L, Prakash S, Todo T, Walker GC, Wang Z, Woodgate R., Mol. Cell 8(1), 2001
PMID: 11515498

AUTHOR UNKNOWN, DNA REPAIR AMST 2(), 2003
Promoters of Corynebacterium glutamicum.
Patek M, Nesvera J, Guyonvarch A, Reyes O, Leblon G., J. Biotechnol. 104(1-3), 2003
PMID: 12948648
A novel method for accurate operon predictions in all sequenced prokaryotes.
Price MN, Huang KH, Alm EJ, Arkin AP., Nucleic Acids Res. 33(3), 2005
PMID: 15701760
The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA.
Rand L, Hinds J, Springer B, Sander P, Buxton RS, Davis EO., Mol. Microbiol. 50(3), 2003
PMID: 14617159
Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies.
Rigali S, Derouaux A, Giannotta F, Dusart J., J. Biol. Chem. 277(15), 2001
PMID: 11756427

AUTHOR UNKNOWN, Gene 145(), 1994

AUTHOR UNKNOWN, Biochimie 73(), 1991
Network motifs in the transcriptional regulation network of Escherichia coli.
Shen-Orr SS, Milo R, Mangan S, Alon U., Nat. Genet. 31(1), 2002
PMID: 11967538
Lysine-156 and serine-119 are required for LexA repressor cleavage: a possible mechanism.
Slilaty SN, Little JW., Proc. Natl. Acad. Sci. U.S.A. 84(12), 1987
PMID: 3108885
Homing endonuclease structure and function.
Stoddard BL., Q. Rev. Biophys. 38(1), 2005
PMID: 16336743
Escherichia coli RecX inhibits RecA recombinase and coprotease activities in vitro and in vivo.
Stohl EA, Brockman JP, Burkle KL, Morimatsu K, Kowalczykowski SC, Seifert HS., J. Biol. Chem. 278(4), 2002
PMID: 12427742
Use of T7 RNA polymerase to direct expression of cloned genes.
Studier FW, Rosenberg AH, Dunn JJ, Dubendorff JW., Meth. Enzymol. 185(), 1990
PMID: 2199796
Rhodobacter sphaeroides LexA has dual activity: optimising and repressing recA gene transcription.
Tapias A, Fernandez S, Alonso JC, Barbe J., Nucleic Acids Res. 30(7), 2002
PMID: 11917014
Corynebacterium glutamicum DNA is subjected to methylation-restriction in Escherichia coli.
Tauch A, Kirchner O, Wehmeier L, Kalinowski J, Puhler A., FEMS Microbiol. Lett. 123(3), 1994
PMID: 7988915

AUTHOR UNKNOWN, Plasmid 34(), 1995
Efficient electrotransformation of corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1.
Tauch A, Kirchner O, Loffler B, Gotker S, Puhler A, Kalinowski J., Curr. Microbiol. 45(5), 2002
PMID: 12232668
Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids.
Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH, Arnold W, Blom J, Brinkrolf K, Brune I, Gotker S, Weisshaar B, Goesmann A, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18430482
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG., Nucleic Acids Res. 25(24), 1997
PMID: 9396791
NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes.
Torrents E, Grinberg I, Gorovitz-Harris B, Lundstrom H, Borovok I, Aharonowitz Y, Sjoberg BM, Cohen G., J. Bacteriol. 189(14), 2007
PMID: 17496099

Walker, Microbiol. Mol. Biol. Rev. 48(1), 1984
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.
Wittkop T, Baumbach J, Lobo FP, Rahmann S., BMC Bioinformatics 8(), 2007
PMID: 17941985

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