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Dulermo R, Onodera T, Coste G, Passot F, Dutertre M, Porteron M, Confalonieri F, Sommer S, Pasternak C. Identification of new genes contributing to the extreme radioresistance of Deinococcus radiodurans using a Tn5-based transposon mutant library. PLoS One 2015; 10:e0124358. [PMID: 25884619 PMCID: PMC4401554 DOI: 10.1371/journal.pone.0124358] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/02/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we have developed an extremely efficient in vivo Tn5-based mutagenesis procedure to construct a Deinococcus radiodurans insertion mutant library subsequently screened for sensitivity to genotoxic agents such as γ and UV radiations or mitomycin C. The genes inactivated in radiosensitive mutants belong to various functional categories, including DNA repair functions, stress responses, signal transduction, membrane transport, several metabolic pathways, and genes of unknown function. Interestingly, preliminary characterization of previously undescribed radiosensitive mutants suggests the contribution of cyclic di-AMP signaling in the recovery of D. radiodurans cells from genotoxic stresses, probably by modulating several pathways involved in the overall cell response. Our analyses also point out a new transcriptional regulator belonging to the GntR family, encoded by DR0265, and a predicted RNase belonging to the newly described Y family, both contributing to the extreme radioresistance of D. radiodurans. Altogether, this work has revealed new cell responses involved either directly or indirectly in repair of various cell damage and confirmed that D. radiodurans extreme radiation resistance is determined by a multiplicity of pathways acting as a complex network.
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Affiliation(s)
- Rémi Dulermo
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Takefumi Onodera
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Geneviève Coste
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Fanny Passot
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Murielle Dutertre
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Martine Porteron
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Fabrice Confalonieri
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Suzanne Sommer
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Cécile Pasternak
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
- * E-mail:
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Vorontsov VV, Sivov IG, Umyarov AM, Sinyashina LN, Karataev GI. Functional activity of transposase of Bordetella pertussis IS element in Escherichia coli cells. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Janion C, Sikora A, Nowosielska A, Grzesiuk E. E. coli BW535, a triple mutant for the DNA repair genes xth, nth, and nfo, chronically induces the SOS response. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2003; 41:237-242. [PMID: 12717778 DOI: 10.1002/em.10154] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A strong chronic induction of the SOS response system occurs in E. coli BW535, a strain defective in nth, nfo and xth genes, and hence severely deficient in the repair of abasic sites in DNA. This was shown here by visualization of filamentous growth of the BW535 strain and by measuring the level of beta-galactosidase expressed in BW535/pSK1002 in comparison to the AB1157/pSK1002 strain. The plasmid pSK1002 bears an umuC::lacZ fusion in which lacZ is under the control of the umuC promoter and regulated under the SOS regulon. Increases in the expression of beta-galactosidase occur in BW535 without any exogenous SOS inducer. Chronic induction of the SOS response was observed previously in E. coli strains bearing mutations in certain genes that have mutator activity and BW535 is a moderate mutator strain. However, not all mutators show this property, since chronic induction of SOS was not observed in mutT or mutY mutators. MutT and MutY proteins, when active, protect bacteria from mutations induced by 8-oxoG lesions in DNA. This suggests that accumulation of abasic sites, but not 8-oxoG residues in DNA, induce the SOS response.
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Affiliation(s)
- Celina Janion
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Janion C, Sikora A, Nowosielska A, Grzesiuk E. Induction of the SOS response in starved Escherichia coli. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2002; 40:129-133. [PMID: 12203406 DOI: 10.1002/em.10094] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The SOS system in Escherichia coli is induced in response to DNA damage and the arrest of DNA synthesis. Here we show that in AB1157 bacteria starved for arginine, conditions for induction of adaptive mutations, the LexA-dependent SOS system is induced, but that this occurs only when the bacteria resume growth and when the source of carbon is glycerol rather than glucose (glycerol, but not glucose, enables synthesis of cAMP). Therefore, we conclude that starved cells accumulate some lesions in DNA, which in growth conditions may trigger SOS induction by a process that is cAMP-dependent.
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Affiliation(s)
- Celina Janion
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Grzesiuk E, Laubitz D, Wójcik-Sikora A, Zabielski R, Pierzynowski SG. Influence of intestinal myoelectrical activity on the growth of Escherichia coli. Bioelectromagnetics 2001; 22:449-55. [PMID: 11536286 DOI: 10.1002/bem.72] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Intestinal bacteria, particularly those adhering to intestinal epithelial cells, are exposed to electric fields and currents generated by the muscular activity of the small intestine. This activity displays a regular pattern known as the myoelectrical migrating complex (MMC). In order to explore the possibility that these endogenous electric fields could affect bacterial growth, a digitised duodenal signal obtained via serosal electrodes from a healthy calf was recorded and then applied via platinum electrodes to Escherichia coli cultures. The culture tubes were placed within a Faraday shield, incubated at 37 degrees C with shaking, and stimulated by the electric current for 5 or 8 h. The growth of E. coli stimulated by the electric current was significantly altered compared to those of non-stimulated controls: after a period of intensive growth, inhibition of cell division was observed. This was not the case when the bacteria with lon mutation were used. Moreover, synchronic bacterial culture could not be achieved in the presence of the MMC-related electric field. These results suggest that the myoelectrical activity of the duodenum, through action on cell membrane, can affect cell division of intestinal bacteria.
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Affiliation(s)
- E Grzesiuk
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
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Broccoli S, Phoenix P, Drolet M. Isolation of the topB gene encoding DNA topoisomerase III as a multicopy suppressor of topA null mutations in Escherichia coli. Mol Microbiol 2000; 35:58-68. [PMID: 10632877 DOI: 10.1046/j.1365-2958.2000.01671.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
One major function of DNA topoisomerase I in Escherichia coli is to repress R-loop formation during transcription elongation, which may otherwise inhibit cell growth. We have previously shown that the growth problems of topA mutants can be corrected by overproducing RNase H, an enzyme that degrades the RNA moiety of an R-loop. The goal of the present study was to identify other potential regulators of R-loop formation. To this end, we have screened for multicopy suppressors of topA null mutations. As expected using this procedure, we cloned the rnhA gene encoding RNase H. In addition, we also identified the topB gene encoding DNA topoisomerase III as an efficient suppressor of topA null mutations and, hence, of R-loop formation. We show that DNA topoisomerase III is able to relax transcription-induced negative supercoiling both in vitro and in vivo. An R-loop is also shown to be a hot-spot for relaxation by DNA topoisomerase III, and we found that R-loop-dependent hypernegative supercoiling can be prevented by the activity of this topoisomerase in vivo. It is also shown that the topB gene can act synergistically with the rnhA gene to correct the growth defect of topA null mutants efficiently. This synergistic effect can be explained by the fact that some R-loops must not be degraded in order for the RNA to be available for protein synthesis. Topoisomerase III can presumably repress the formation of such R-loops or cause their destabilization to prevent RNA degradation. This is supported by the fact that overproduction of this topoisomerase corrects the negative effect of overexpressing RNase H activity on the growth of topA null mutants at low temperatures. Moreover, the fact that DNA topoisomerase III does not relax global supercoiling supports our previous conclusion that R-loop formation, and therefore the essential function of DNA topoisomerase I, involves local, rather than global, supercoiling.
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Affiliation(s)
- S Broccoli
- D¿epartement de microbiologie et immunologie, Universit¿e de Montr¿eal, CP 6128, succursale centre-ville, Montr¿eal, Qu¿ebec, Canada, H3C 3J7
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Clément JM, Wilde C, Bachellier S, Lambert P, Hofnung M. IS1397 is active for transposition into the chromosome of Escherichia coli K-12 and inserts specifically into palindromic units of bacterial interspersed mosaic elements. J Bacteriol 1999; 181:6929-36. [PMID: 10559158 PMCID: PMC94167 DOI: 10.1128/jb.181.22.6929-6936.1999] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We demonstrate that IS1397, a putative mobile genetic element discovered in natural isolates of Escherichia coli, is active for transposition into the chromosome of E. coli K-12 and inserts specifically into palindromic units, also called repetitive extragenic palindromes, the basic element of bacterial interspersed mosaic elements (BIMEs), which are found in intergenic regions of enterobacteria closely related to E. coli and Salmonella. We could not detect transposition onto a plasmid carrying BIMEs. This unprecedented specificity of insertion into a well-characterized chromosomal intergenic repeated element and its evolutionary implications are discussed.
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Affiliation(s)
- J M Clément
- Unité de Programmation Moléculaire et Toxicologie Génétique, CNRS URA 1444, Institut Pasteur, 75724 Paris Cedex 15, France.
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Yigit H, Reznikoff WS. Escherichia coli DNA topoisomerase I copurifies with Tn5 transposase, and Tn5 transposase inhibits topoisomerase I. J Bacteriol 1999; 181:3185-92. [PMID: 10322021 PMCID: PMC93775 DOI: 10.1128/jb.181.10.3185-3192.1999] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tn5 transposase (Tnp) overproduction is lethal to Escherichia coli. Genetic evidence suggested that this killing involves titration of E. coli topoisomerase I (Topo I). Here, we present biochemical evidence that supports this model. Tn5 Tnp copurifies with Topo I while nonkilling derivatives of Tnp, Delta37Tnp and Delta55Tnp (Inhibitor [Inh]), show reduced affinity or no affinity, respectively, for Topo I. In agreement with these results, the presence of Tnp, but not Delta37 or Inh derivatives of Tnp, inhibits the DNA relaxation activity of Topo I in vivo as well as in vitro. Other proteins, including RNA polymerase, are also found to copurify with Tnp. For RNA polymerase, reduced copurification with Tnp is observed in extracts from a topA mutant strain, suggesting that RNA polymerase interacts with Topo I and not Tnp.
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MESH Headings
- Bacterial Proteins/metabolism
- Blotting, Western
- Chromatography, Affinity
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/isolation & purification
- DNA Topoisomerases, Type I/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/metabolism
- DNA-Directed RNA Polymerases/metabolism
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Genes, Bacterial
- Genes, Lethal
- Molecular Weight
- Nucleic Acid Conformation
- Plasmids/chemistry
- Plasmids/metabolism
- Protein Binding
- Recombinant Fusion Proteins/metabolism
- Sequence Deletion
- Suppression, Genetic
- Topoisomerase I Inhibitors
- Transposases/genetics
- Transposases/isolation & purification
- Transposases/metabolism
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Affiliation(s)
- H Yigit
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Yigit H, Reznikoff WS. Escherichia coli DNA topoisomerase I and suppression of killing by Tn5 transposase overproduction: topoisomerase I modulates Tn5 transposition. J Bacteriol 1998; 180:5866-74. [PMID: 9811643 PMCID: PMC107659 DOI: 10.1128/jb.180.22.5866-5874.1998] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tn5 transposase (Tnp) overproduction is lethal to Escherichia coli. The overproduction causes cell filamentation and abnormal chromosome segregation. Here we present three lines of evidence strongly suggesting that Tnp overproduction killing is due to titration of topoisomerase I. First, a suppressor mutation of transposase overproduction killing, stkD10, is localized in topA (the gene for topoisomerase I). The stkD10 mutant has the following characteristics: first, it has an increased abundance of topoisomerase I protein, the topoisomerase I is defective for the DNA relaxation activity, and DNA gyrase activity is reduced; second, the suppressor phenotype of a second mutation localized in rpoH, stkA14 (H. Yigit and W. S. Reznikoff, J. Bacteriol. 179:1704-1713, 1997), can be explained by an increase in topA expression; and third, overexpression of wild-type topA partially suppresses the killing. Finally, topoisomerase I was found to enhance Tn5 transposition up to 30-fold in vivo.
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Affiliation(s)
- H Yigit
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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