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Sass TH, Lovett ST. The DNA damage response of Escherichia coli, revisited: Differential gene expression after replication inhibition. Proc Natl Acad Sci U S A 2024; 121:e2407832121. [PMID: 38935560 PMCID: PMC11228462 DOI: 10.1073/pnas.2407832121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
In 1967, in this journal, Evelyn Witkin proposed the existence of a coordinated DNA damage response in Escherichia coli, which later came to be called the "SOS response." We revisited this response using the replication inhibitor azidothymidine (AZT) and RNA-Seq analysis and identified several features. We confirm the induction of classic Save our ship (SOS) loci and identify several genes, including many of the pyrimidine pathway, that have not been previously demonstrated to be DNA damage-inducible. Despite a strong dependence on LexA, these genes lack LexA boxes and their regulation by LexA is likely to be indirect via unknown factors. We show that the transcription factor "stringent starvation protein" SspA is as important as LexA in the regulation of AZT-induced genes and that the genes activated by SspA change dramatically after AZT exposure. Our experiments identify additional LexA-independent DNA damage inducible genes, including 22 small RNA genes, some of which appear to activated by SspA. Motility and chemotaxis genes are strongly down-regulated by AZT, possibly as a result of one of more of the small RNAs or other transcription factors such as AppY and GadE, whose expression is elevated by AZT. Genes controlling the iron siderophore, enterobactin, and iron homeostasis are also strongly induced, independent of LexA. We confirm that IraD antiadaptor protein is induced independent of LexA and that a second antiadaptor, IraM is likewise strongly AZT-inducible, independent of LexA, suggesting that RpoS stabilization via these antiadaptor proteins is an integral part of replication stress tolerance.
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Affiliation(s)
- Thalia H Sass
- Department of Biology, Brandeis University, Waltham, MA 02454-9110
- Rosenstiel Basic Medical Sciences Research Center MS029, Brandeis University, Waltham, MA 02454-9110
| | - Susan T Lovett
- Department of Biology, Brandeis University, Waltham, MA 02454-9110
- Rosenstiel Basic Medical Sciences Research Center MS029, Brandeis University, Waltham, MA 02454-9110
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Feliciello I, Đermić E, Malović H, Ivanković S, Zahradka D, Ljubić S, Procino A, Đermić D. Regulation of ssb Gene Expression in Escherichia coli. Int J Mol Sci 2022; 23:ijms231810917. [PMID: 36142827 PMCID: PMC9505508 DOI: 10.3390/ijms231810917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/01/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial SSB proteins, as well as their eukaryotic RPA analogues, are essential and ubiquitous. They avidly bind single-stranded DNA and regulate/coordinate its metabolism, hence enabling essential DNA processes such as replication, transcription, and repair. The prototypic Escherichia coli SSB protein is encoded by an ssb gene. Although the ssb gene promoters harbor an SOS box, multiple studies over several decades failed to elucidate whether ssb gene expression is inducible and SOS dependent. The SOS regulon is comprised of about 50 genes, whose transcription is coordinately induced under stress conditions. Using quantitative real-time PCR, we determined the ssb gene expression kinetics in UV- and γ-irradiated E. coli and revealed that ssb gene expression is elevated in irradiated cells in an SOS-dependent manner. Additionally, the expression of the sulA gene was determined to indicate the extent of SOS induction. In a mutant with a constitutively induced SOS regulon, the ssb gene was overexpressed in the absence of DNA damage. Furthermore, we measured ssb gene expression by droplet digital PCR during unaffected bacterial growth and revealed that ssb gene expression was equal in wild-type and SOS- bacteria, whereas sulA expression was higher in the former. This study thus reveals a complex pattern of ssb gene expression, which under stress conditions depends on the SOS regulon, whereas during normal bacterial growth it is unlinked to SOS induction. The E. coli ssb gene is SOS regulated in such a way that its basal expression is relatively high and can be increased only through stronger SOS induction. The remarkable SOS induction observed in undisturbed wild-type cells may challenge our notion of the physiological role of the SOS response in bacteria.
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Affiliation(s)
- Isidoro Feliciello
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 81031 Naples, Italy
| | - Edyta Đermić
- Department of Plant Pathology, Division for Phytomedicine, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia
| | - Helena Malović
- Department of Plant Pathology, Division for Phytomedicine, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia
| | - Siniša Ivanković
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Davor Zahradka
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Sven Ljubić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Alfredo Procino
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Damir Đermić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
- Correspondence:
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Kaushik V, Tiwari M, Tiwari V. Interaction of RecA mediated SOS response with bacterial persistence, biofilm formation, and host response. Int J Biol Macromol 2022; 217:931-943. [PMID: 35905765 DOI: 10.1016/j.ijbiomac.2022.07.176] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Antibiotics have a primary mode of actions, and most of them have a common secondary mode of action via reactive species (ROS and RNS) mediated DNA damage. Bacteria have been able to tolerate this DNA damage by SOS (Save-Our-Soul) response. RecA is the universal essential key protein of the DNA damage mediated SOS repair in various bacteria including ESKAPE pathogens. In addition, antibiotics also triggers activation of various other bacterial mechanisms such as biofilm formation, host dependent responses, persister subpopulation formation. These supporting the survival of bacteria in unfriendly natural conditions i.e. antibiotic presence. This review highlights the detailed mechanism of RecA mediated SOS response as well as role of RecA-LexA interaction in SOS response. The review also focuses on inter-connection between DNA damage repair pathway (like SOS response) with other survival mechanisms of bacteria such as host mediated RecA induction, persister-SOS interplay, and biofilm-SOS interplay. This understanding of inter-connection of SOS response with different other survival mechanisms will prove beneficial in targeting the SOS response for prevention and development of therapeutics against recalcitrant bacterial infections. The review also covers the significance of RecA as a promising potent therapeutic target for hindering bacterial SOS response in prevailing successful treatments of bacterial infections and enhancing the conventional antibiotic efficiency.
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Affiliation(s)
- Vaishali Kaushik
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India.
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Wendel BM, Hollingsworth S, Courcelle CT, Courcelle J. UV-induced DNA damage disrupts the coordination between replication initiation, elongation and completion. Genes Cells 2021; 26:94-108. [PMID: 33382157 DOI: 10.1111/gtc.12826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 11/28/2022]
Abstract
Replication initiation, elongation and completion are tightly coordinated to ensure that all sequences replicate precisely once each generation. UV-induced DNA damage disrupts replication and delays elongation, which may compromise this coordination leading to genome instability and cell death. Here, we profiled the Escherichia coli genome as it recovers from UV irradiation to determine how these replicational processes respond. We show that oriC initiations continue to occur, leading to copy number enrichments in this region. At late times, the combination of new oriC initiations and delayed elongating forks converging in the terminus appear to stress or impair the completion reaction, leading to a transient over-replication in this region of the chromosome. In mutants impaired for restoring elongation, including recA, recF and uvrA, the genome degrades or remains static, suggesting that cell death occurs early after replication is disrupted, leaving partially duplicated genomes. In mutants impaired for completing replication, including recBC, sbcCD xonA and recG, the recovery of elongation and initiation leads to a bottleneck, where the nonterminus region of the genome is amplified and accumulates, indicating that a delayed cell death occurs in these mutants, likely resulting from mis-segregation of unbalanced or unresolved chromosomes when cells divide.
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Affiliation(s)
- Brian M Wendel
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | | | - Justin Courcelle
- Department of Biology, Portland State University, Portland, OR, USA
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Wu VM, Huynh E, Tang S, Uskoković V. Calcium phosphate nanoparticles as intrinsic inorganic antimicrobials: mechanism of action. Biomed Mater 2020; 16:015018. [DOI: 10.1088/1748-605x/aba281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Abstract
All organisms possess a diverse set of genetic programs that are used to alter cellular physiology in response to environmental cues. The gram-negative bacterium, Escherichia coli, mounts what is known as the "SOS response" following DNA damage, replication fork arrest, and a myriad of other environmental stresses. For over 50 years, E. coli has served as the paradigm for our understanding of the transcriptional, and physiological changes that occur following DNA damage (400). In this chapter, we summarize the current view of the SOS response and discuss how this genetic circuit is regulated. In addition to examining the E. coli SOS response, we also include a discussion of the SOS regulatory networks in other bacteria to provide a broader perspective on how prokaryotes respond to DNA damage.
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Herrick J, Sclavi B. Ribonucleotide reductase and the regulation of DNA replication: an old story and an ancient heritage. Mol Microbiol 2007; 63:22-34. [PMID: 17229208 DOI: 10.1111/j.1365-2958.2006.05493.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All organisms that synthesize their own DNA have evolved mechanisms for maintaining a constant DNA/cell mass ratio independent of growth rate. The DNA/cell mass ratio is a central parameter in the processes controlling the cell cycle. The co-ordination of DNA replication with cell growth involves multiple levels of regulation. DNA synthesis is initiated at specific sites on the chromosome termed origins of replication, and proceeds bidirectionally to elongate and duplicate the chromosome. These two processes, initiation and elongation, therefore determine the total rate of DNA synthesis in the cell. In Escherichia coli, initiation depends on the DnaA protein while elongation depends on a multiprotein replication factory that incorporates deoxyribonucleotides (dNTPs) into the growing DNA chain. The enzyme ribonucleotide reductase (RNR) is universally responsible for synthesizing the necessary dNTPs. In this review we examine the role RNR plays in regulating the total rate of DNA synthesis in E. coli and, hence, in maintaining constant DNA/cell mass ratios during normal growth and under conditions of DNA stress.
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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August PR, Rahn JA, Flickinger MC, Sherman DH. Inducible synthesis of the mitomycin C resistance gene product (MCRA) from Streptomyces lavendulae. Gene 1996; 175:261-7. [PMID: 8917108 DOI: 10.1016/0378-1119(96)00172-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The mcr locus from Streptomyces lavendulae confers high level resistance (> 100 micrograms/ml) to mitomycin C (MC) and related mitomycins when cloned into Streptomyces lividans. Production of the mcrA gene product (MCRA) was shown to be MC-inducible by identification of MCRA (M(r) of 54 kDa) using Western blot analysis and enzyme linked immunosorbent assay (ELISA). The magnitude of MCRA production was dependent on MC concentration, with primary induction starting at 0.1 microgram/ml and maximum induction at 10 micrograms/ml of the drug. Different levels of MCRA production were observed when other mitomycin metabolites were used as inducers, and the level of induction related directly to aziridine ring substitution on the individual molecules. Moreover, inducible synthesis of the mcr A gene product was unique to this structural class since production of MCRA did not occur as a general response to DNA damaging agents. The time profile of intracellular MCRA synthesis correlated with MC production in S. lavendulae, suggesting coordinated regulation of MC resistance and biosynthetic genes.
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Affiliation(s)
- P R August
- Department of Microbiology, University of Minnesota, St. Paul 55108, USA
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Paz-Elizur T, Skaliter R, Blumenstein S, Livneh Z. β*, a UV-inducible Smaller Form of the β Subunit Sliding Clamp of DNA Polymerase III of Escherichia coli. J Biol Chem 1996. [DOI: 10.1074/jbc.271.5.2482] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Kleinsteuber S, Quiñones A. Expression of the dnaB gene of Escherichia coli is inducible by replication-blocking DNA damage in a recA-independent manner. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:695-702. [PMID: 7476872 DOI: 10.1007/bf02191709] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The replicative DNA helicase encoded by the dnaB gene is essential for chromosomal DNA replication in Escherichia coli. The DnaB protein is a component of the phi X-type primosome which is regarded as a model system for lagging strand synthesis of the chromosome. Using translational lacZ fusions at the plasmid and chromosomal levels, we studied the influence of DNA-damaging agents on dnaB gene expression. We found that DNA damage caused by mitomycin C, methyl methanesulphonate, 4-nitro-quinoline N-oxide, and UV irradiation led to a moderate, but significant induction of dnaB gene expression. Comparative S1 analysis of transcripts in untreated and induced cells demonstrated that the induction is due to increased transcription from the dnaB promoter. In contrast to other DNA damage-inducible replication genes, such as dnaA, dnaN, dnaQ, and polA, expression of which is not inducible in recA and lexA mutants, the induction of dnaB was also observed in a recA1 mutant. These results show that the induction of dnaB gene expression by replication-blocking DNA damage is due to a mechanism other than the indirectly SOS-dependent induction of the other DNA replication genes. Moreover, the data suggest that replication proteins are involved in recovery from replication-blocking DNA damage in two different ways--on the one hand at the level of initiation and on the other hand at the level of elongation.
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Affiliation(s)
- S Kleinsteuber
- Institut für Genetik, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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Zakrzewska-Czerwińska J, Nardmann J, Schrempf H. Inducible transcription of the dnaA gene from Streptomyces lividans 66. MOLECULAR & GENERAL GENETICS : MGG 1994; 242:440-7. [PMID: 8121399 DOI: 10.1007/bf00281794] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The dnaA gene of Streptomyces lividans was cloned using the Escherichia coli medium-copy-number vector pSU18 and E. coli strain TC1963, which can by-pass the requirement for the DnaA protein. Its regulatory region was subcloned in the Streptomyces probe vector pIJ4083. Primer extension and S1 mapping studies allowed the identification of a class I Streptomyces promotor (P2). An additional, previously unknown promoter type (P1) was found by S1 mapping. The presence of two DnaA box motifs between P1 and P2 suggests that the transcriptions of the S. lividans dnaA gene is autoregulated by its gene product. It was shown that the transcription of the dnaA gene is significantly induced by mitomycin C, an agent known to inhibit DNA replication. The data suggest that, as in E. coli, one of the regulatory mechanisms governing the transcription of the dnaA gene in S. lividans is probably related to the SOS response network.
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Affiliation(s)
- J Zakrzewska-Czerwińska
- Department of Microbiology, Institute of Immunology and Experimental Therapy, Wrocław, Poland
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Woelker B, Messer W. The structure of the initiation complex at the replication origin, oriC, of Escherichia coli. Nucleic Acids Res 1993; 21:5025-33. [PMID: 8255756 PMCID: PMC310613 DOI: 10.1093/nar/21.22.5025] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Two distinct regions in the replication origin, oriC, of Escherichia coli are separately distorted upon initiation complex formation by the initiator protein DnaA. The AT-rich region in the left part of oriC and the start site region in the right part of oriC. Chemical modification of single-stranded DNA was observed at both regions whereas endonuclease recognition of DNA mini-bulges specifically occurred in the start site region. We show that the helical phasing of binding sites for DnaA protein in oriC is important for origin function. An insertion or deletion of one helical turn between the two rightmost binding sites does not alter the efficiency of replication initiation, whereas all modifications of distance by less or more than one helical turn result in inactivation of oriC. DnaA binding and helical distortions in the AT-rich region as well as in the start site region are not affected in the distance mutants irrespective of their functionality in vivo. We propose a specific compact nucleoprotein structure for the initiation complex.
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Affiliation(s)
- B Woelker
- Max-Planck-Institut für Molekulare Genetik, Berlin-Dahlem, Germany
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14
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Abstract
Following exposure to UV light DNA replication stops and then resumes. The SOS response is required for the restoration of replication. Replication recovery occurs in lexA(Ind) cells carrying a high constitutive level of RecA protein. Replication is also affected by UmuCD proteins, photoreactivation, and excision repair. In addition, there is a constitutive and recA independent way to replicate over UV photoproducts associated with the production of gaps in daughter DNA strands. There are two ways to account for the replication in UV-irradiated cells. A stalled replication fork can be reactivated. Alternatively, a replication fork could be destroyed irreparably, with no available way to complete the round of replication. In that case, postirradiation replication could be due exclusively to replication forks assembled de novo at the origin(s). Changes in replication initiation are observed following UV irradiation. Initiations are first inhibited and then stimulated. They become independent of de novo protein synthesis and sometimes do not stop in dnaA(ts) mutants shifted to 42 degrees C. Although the inducible functions are involved in the recovery of replication at different levels of UV damage, some modifications of the replication initiation mechanism appear to be specific to severely damaged cells. Such modifications seem to include the dnaA(ts) independence for initiations and the transient initiation inhibition. RecA protein can be directly involved both in the modification of initiation and in reactivation of the stalled replication forks. Although the restoration of replication depends on the SOS response a synthesis of some protein(s) that do not belong to the LexA regulon seems to be required as well. These proteins can be under RecA control and one of their functions may be to inhibit the rnhA gene. Certain recA mutations may selectively affect different mechanisms of the replication recovery (namely, recA430, recA727, recA718, recA1730). Overproduction of the photoreactivating enzyme in the dark could influence UmuCD activity in replication. The UmuCD function appears to be blocked in strains carrying the dnaE1026 mutation or overproducing the dnaQ protein. For some unknown reason the UmuCD-associated replication mechanism is the only one available for phage with damaged DNA.
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Lewis LK, Jenkins ME, Mount DW. Isolation of DNA damage-inducible promoters in Escherichia coli: regulation of polB (dinA), dinG, and dinH by LexA repressor. J Bacteriol 1992; 174:3377-85. [PMID: 1577702 PMCID: PMC206008 DOI: 10.1128/jb.174.10.3377-3385.1992] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A new genetic screening method has been developed to isolate Escherichia coli promoters which are components of the SOS regulon. Plasmids containing the regulatory regions of polB (dinA) and two new loci, dinG and dinH, were characterized. Galactokinase gene fusion experiments indicated that transcription of these genes is inducible by treatment with mitomycin and conforms to a classical model of SOS regulation involving simple LexA repression. Mapping studies using the E. coli DNA library of Kohara et al. (Y. Kohara, K. Akiyama, and K. Isono, Cell 50:495-508, 1987) revealed that dinG and dinH are located at 17.8 and 19.8 min on the chromosome, respectively. The nucleotide sequence of the dinH regulatory region contains a segment which is very similar to previously characterized binding sites for LexA protein. An asymmetric, noncanonical 20-bp LexA operator in the cloned dinG promoter region was identified. Additional experiments have revealed that the nucleotide sequence of the gene immediately downstream of the DNA damage-inducible polB locus encodes a polypeptide which has extensive sequence homology to several known and putative DNA and RNA helicase proteins. This gene, which is not regulated by the LexA repressor, has been designated hepA. The predicted amino acid sequence of the product of hepA contains several highly conserved sequence motifs that are also found in enzymes such as the RecQ and UvrB proteins of E. coli and the Rad3 protein of Saccharomyces cerevisiae.
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Affiliation(s)
- L K Lewis
- Molecular and Cellular Biology Department, University of Arizona, Tucson 85721
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Holz A, Schaefer C, Gille H, Jueterbock WR, Messer W. Mutations in the DnaA binding sites of the replication origin of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1992; 233:81-8. [PMID: 1603077 DOI: 10.1007/bf00587564] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mutations (base changes) were introduced into the four DnaA binding sites (DnaA boxes) of the Escherichia coli replication origin, oriC. Mutations in a single DnaA box did not impair the ability of these origins to replicate in vivo and in vitro. A combination of mutations in two DnaA boxes, R1 and R4, resulted in slower growth of the oriC plasmid-bearing host cells. DnaA protein interaction with mutant and wild-type DnaA boxes was analyzed by DNase I footprinting. Binding of DnaA protein to a mutated DnaA box R1 was not affected by a mutation in DnaA box R4 and vice versa. Mutations in DnaA boxes R1 and R4 did not modify the ability of the DnaA protein to bind to other DnaA boxes in oriC.
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Affiliation(s)
- A Holz
- Max-Planck-Institut für Molekulare Genetik, Berlin, FRG
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17
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Rinken R, Wackernagel W. Inhibition of the recBCD-dependent activation of Chi recombinational hot spots in SOS-induced cells of Escherichia coli. J Bacteriol 1992; 174:1172-8. [PMID: 1310498 PMCID: PMC206409 DOI: 10.1128/jb.174.4.1172-1178.1992] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nucleotide sequences called Chi (5'-GCTGGTGG-3') enhance homologous recombination near their location by the RecBCD enzyme in Escherichia coli (Chi activation). A partial inhibition of Chi activation measured in lambda red gam mutant crosses was observed after treatment of wild-type cells with DNA-damaging agents including UV, mitomycin, and nalidixic acid. Inhibition of Chi activation was not accompanied by an overall decrease of recombination. A lexA3 mutation which blocks induction of the SOS system prevented the inhibition of Chi activation, indicating that an SOS function could be responsible for the inhibition. Overproduction of the RecD subunit of the RecBCD enzyme from a multicopy plasmid carrying the recD gene prevented the induced inhibition of Chi activation, whereas overproduction of RecB or RecC subunits did not. It is proposed that in SOS-induced cells the RecBCD enzyme is modified into a Chi-independent recombination enzyme, with the RecD subunit being the regulatory switch key.
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Affiliation(s)
- R Rinken
- Genetik, Fachbereich Biologie, Universität Oldenburg, Germany
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Wende M, Quinones A, Diederich L, Jueterbock WR, Messer W. Transcription termination in the dnaA gene. MOLECULAR & GENERAL GENETICS : MGG 1991; 230:486-90. [PMID: 1766443 DOI: 10.1007/bf00280306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The termination of transcription in the dnaA gene of E. coli was analyzed using transcriptional fusions to the galactokinase gene, S1 nuclease mapping and quantification of translation products by Western blots. The majority of transcripts originating from dnaA promoters terminated at several positions within a 200 bp region inside the dnaA reading frame.
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Affiliation(s)
- M Wende
- Max-Planck-Institut für molekulare Genetik, Berlin, FRG
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19
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Quiñones A, Jueterbock WR, Messer W. DNA lesions that block DNA replication are responsible for the dnaA induction caused by DNA damage. MOLECULAR & GENERAL GENETICS : MGG 1991; 231:81-7. [PMID: 1753947 DOI: 10.1007/bf00293825] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The initiation protein DnaA of Escherichia coli regulates its own expression autogenously by binding to a 9 bp consensus sequence, the dnaA box, between the promoters dnaAP1 and dnaAP2. In this study, we analysed dnaA regulation in relation to DNA damage and found dnaA expression to be inducible by DNA lesions that inhibit DNA replication. On the other hand, coding DNA lesions were not able to induce dnaA expression. These results suggest that an additional regulatory mechanism is involved in dnaA gene expression and that DnaA protein may play a role in cellular responses to DNA damage. Furthermore, they strongly suggest that in response to DNA replication inhibition by DNA damage, and enhanced (re)initiation capacity is induced by oriC.
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Affiliation(s)
- A Quiñones
- Institut für Genetik, Martin-Luther-Universität, Halle/S., FRG
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Weinreich MD, Makris JC, Reznikoff WS. Induction of the SOS response in Escherichia coli inhibits Tn5 and IS50 transposition. J Bacteriol 1991; 173:6910-8. [PMID: 1657870 PMCID: PMC209045 DOI: 10.1128/jb.173.21.6910-6918.1991] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In response to DNA damage or the inhibition of normal DNA replication in Escherichia coli, a set of some 20 unlinked operons is induced through the RecA-mediated cleavage of the LexA repressor. We examined the effect of this SOS response on the transposition of Tn5 and determined that the frequency of transposition is reduced 5- to 10-fold in cells that constitutively express SOS functions, e.g., lexA(Def) strains. Furthermore, this inhibition is independent of recA function, is fully reversed by a wild-type copy of lexA, and is not caused by an alteration in the levels of the Tn5 transposase or inhibitor proteins. We isolated insertion mutations in a lexA(Def) background that reverse this transposition defect; all of these mapped to a new locus near 23 min on the E. coli chromosome.
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Affiliation(s)
- M D Weinreich
- Department of Biochemistry, University of Wisconsin, Madison 53706
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Gille H, Egan JB, Roth A, Messer W. The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res 1991; 19:4167-72. [PMID: 1870971 PMCID: PMC328557 DOI: 10.1093/nar/19.15.4167] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The FIS protein (factor for inversion stimulation) is known to stimulate site-specific recombination processes, such as the inversion of the G segment of bacteriophage Mu, by binding to specific enhancer sequences. It has also been shown to activate transcription from rRNA promoters both in vitro and in vivo. We have identified a specific binding site for FIS in the center of the origin of chromosomal DNA replication, oriC. The DNA bends upon FIS binding. Occupation of the FIS site and binding of DnaA, the initiator protein, to its adjacent binding site (R3) are mutually exclusive. A fis mutant strain can not be efficiently transformed with plasmids which carry and replicate from oriC, suggesting that FIS is required for minichromosome replication.
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Affiliation(s)
- H Gille
- Max-Planck-Institut für Molekulare Genetik, Berlin, FRG
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