<i>Escherichia coli</i> HU protein suppresses DNA‐gyrase‐mediated illegitimate recombination and SOS induction

Shanado, Yuka; Kato, Junichi; Ikeda, Hideo

doi:10.1046/j.1365-2443.1998.00208.x

Cited by 15 publications

(8 citation statements)

References 33 publications

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“…Also, an important role for the translesion polymerases, in particular PolIV, has been shown for frameshift mutations (36), and in deletion formation between long tandem repeats, but the mechanism of frameshift formation and RecA-dependent homologous recombination is different from that observed for large deletions with no or little homology at deletion endpoints (1,37). In view of previous data, involvement of the LexA regulon and the translesion polymerases in deletion formation is unexpected, because results from specific model systems containing recombining tandem repeats indicate that induction of the SOS response itself does not increase deletion formation (13,16,38). One interpretation of these conflicting results is that deletions formed between tandem repeats are not mediated via the same mechanism as spontaneous deletions in a normal bacterial chromosome.…”

Section: Discussionmentioning

confidence: 98%

Translesion DNA polymerases are required for spontaneous deletion formation in Salmonella typhimurium

Koskiniemi

Andersson

2009

Proc. Natl. Acad. Sci. U.S.A.

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How spontaneous deletions form in bacteria is still a partly unresolved problem. Here, we show that deletion formation in Salmonella typhimurium requires the presence of functional translesion polymerases. First, in wild-type bacteria, removal of the known translesion DNA polymerases, PolII (polB), PolIV (dinB), PolV (umuDC), and SamAB (samAB), resulted in a 10-fold decrease in the deletion rate, indicating that 90% of all spontaneous deletions require these polymerases for their formation. Second, overexpression of these polymerases by derepression of the DNA damage-inducible LexA regulon caused a 25-fold increase in deletion rate that depended on the presence of functional translesion polymerases. Third, overexpression of the polymerases PolII and PolIV from a plasmid increased the deletion rate 12-to 30-fold, respectively. Last, in a recBC ؊ mutant where dsDNA ends are stabilized due to the lack of the end-processing nuclease RecBC, the deletion rate was increased 20-fold. This increase depended on the translesion polymerases. In lexA(def) mutant cells with constitutive SOS expression, a 10-fold increase in DNA breaks was observed. Inactivation of all 4 translesion polymerases in the lexA(def) mutant reduced the deletion rate 250-fold without any concomitant reduction in the amount of DNA breaks. Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in a lexA(def) mutant with a concomitant 50-fold reduction in deletion rate. These findings suggest that the translesion polymerases are not involved in forming the DNA breaks, but that they require them to stimulate deletion formation.bacteria ͉ DNA homology ͉ gene loss ͉ RecA protein S pontaneous deletions are formed at relatively high frequencies in growing bacteria, but they rarely become fixed in the population because of their normally deleterious nature. The different mechanisms that are involved in deletion formation are well described with regard to deletions that form between long sequence homologies, whereas the mechanism for deletion formation involving little or no sequence homology is still quite unclear. Deletion formation can be divided into 3 classes depending on the mechanism of formation. First, deletions can be formed by RecA-dependent homologous recombination, which requires at least 20-40 bp of homology to be effective (1). However, several studies suggest that many spontaneous deletions are formed via RecA-independent pathways (2-4) where short (Ͻ25 bp) or no repeats are found at the deletion endpoints.

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Section: Discussionmentioning

confidence: 98%

Translesion DNA polymerases are required for spontaneous deletion formation in Salmonella typhimurium

Koskiniemi

Andersson

2009

Proc. Natl. Acad. Sci. U.S.A.

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“…4B). Such an idea emerged from studies of quinolonestimulated illegitimate recombination (32,33,66), a phenomenon that is best explained by gyrase subunit dissociation-reassociation (this concept also appears to apply to interactions of eukaryotic topoisomerase II with certain antitumor agents [2] (53). Thus, the mutation appears to shift lethal activity from step d in Fig.…”

Section: Destabilization Of Cleaved Complexesmentioning

confidence: 99%

Quinolone-Mediated Bacterial Death

Drlica¹,

Malik²,

Kerns

et al. 2008

Antimicrob Agents Chemother

497

402

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2The fluoroquinolones are broad-spectrum antibacterial agents that are becoming increasingly popular as bacterial resistance erodes the effectiveness of other agents (fluoroquinolone sales accounted for 18% of the antibacterial market in 2006) (41). One of the attractive features of the quinolones is their ability to kill bacteria rapidly, an ability that differs widely among the various derivatives. For example, quinolones differ in rate and extent of killing, in the need for aerobic metabolism to kill cells, and in the effect of protein synthesis inhibitors on quinolone lethality. Understanding the mechanisms underlying these differences could lead to new ways for identifying the most bactericidal quinolone derivatives.Before describing the types of damage caused by the quinolones, it is useful to define lethal activity. Operationally, it is the ability of drug treatment to reduce the number of viable cells, usually measured as CFU on drug-free agar after treatment. This assay is distinct from measurements that detect inhibition of growth (e.g., MIC), since with the latter bacteria are exposed to drug throughout the measurement. The distinction between killing and blocking growth is important because it allows susceptibility determinations to be related to particular biological processes. For example, inhibition of growth is typically reversed by the removal of drug, while cell death is not. Thus, biochemical events associated with blocking growth should be readily reversible, while those responsible for cell death should be difficult to reverse. Reversibility can be used to distinguish among quinolone derivatives and assign functions to particular aspects of drug structure. Moreover, protective functions, such as repair and stress responses, can be distinguished by whether their absence affects inhibition of growth, killing, or both.The intracellular targets of the quinolones are two DNA topoisomerases: gyrase and topoisomerase IV. Gyrase tends to be the primary target in gram-negative bacteria, while topoisomerase IV is preferentially inhibited by most quinolones in gram-positive organisms (28). Both enzymes use a doublestrand DNA passage mechanism, and it is likely that quinolone biochemistry is similar for both. However, physiological differences between the enzymes exist, some of which may bear on quinolone lethality.In the present minireview we consider cell death through a two-part "poison" hypothesis in which the quinolones form reversible drug-topoisomerase-DNA complexes that subsequently lead to several types of irreversible (lethal) damage. Other consequences of quinolone treatment, such as depletion of gyrase and topoisomerase IV activity, are probably less immediate (42). To provide a framework for considering quinolone lethality, we begin by briefly describing the drug-topoisomerase-DNA complexes. Readers interested in a more comprehensive discussion of quinolones are referred to a previously published work (28). QUINOLONE-TOPOISOMERASE-DNA COMPLEXESAs a normal part of their reaction mechanism, g...

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“…In Salmonella, NAPs have been shown to influence virulence gene expression (Harrison et al, 1994; O'Byrne & Dorman, 1994a, b; Lucchini et al, 2006;Marshall et al, 1999; Navarre et al, 2006;Schechter et al, 2003). HU binds to DNA relatively non-specifically and influences many DNA-based transactions, including replication, transcription, site-specific-, general and illegitimate recombination, transposition and DNA repair (Kamashev et al, 2008;Li & Waters, 1998;Merickel & Johnson, 2004;Ryan et al, 2002;Semsey et al, 2004;Shanado et al, 1998;Signon & Kleckner, 1995). It also has RNA-binding activity (Balandina et al, 2001) and a preference for binding to unusual conformations in DNA such as four-way junctions and extruded cruciform structures (Kamashev et al, 1999;Pontiggia et al, 1993;Swinger & Rice, 2004).…”

Section: Introductionmentioning

confidence: 99%

Nucleoid-associated protein HU controls three regulons that coordinate virulence, response to stress and general physiology in Salmonella enterica serovar Typhimurium

et al. 2011

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The role of the HU nucleoid-associated proteins in gene regulation was examined in Salmonella enterica serovar Typhimurium. The dimeric HU protein consists of different combinations of its a and b subunits. Transcriptomic analysis was performed with cultures growing at 37 6C at 1, 4 and 6 h after inoculation with mutants that lack combinations of HU a and HU b. Distinct but overlapping patterns of gene expression were detected at each time point for each of the three mutants, revealing not one but three regulons of genes controlled by the HU proteins. Mutations in the hup genes altered the expression of regulatory and structural genes in both the SPI1 and SPI2 pathogenicity islands. The hupA hupB double mutant was defective in invasion of epithelial cell lines and in its ability to survive in macrophages. The double mutant also had defective swarming activity and a competitive fitness disadvantage compared with the wild-type. In contrast, inactivation of just the hupB gene resulted in increased fitness and correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures. Our data show that HU coordinates the expression of genes involved in central metabolism and virulence and contributes to the success of S. enterica as a pathogen. INTRODUCTIONThe HU DNA-binding protein is one of approximately 12 nucleoid-associated proteins (NAPs) that have been described in Gram-negative bacteria such as Escherichia coli and Salmonella enterica. NAPs have the potential to influence the expression of large numbers of genes in bacteria and help to organize the nucleoid (Azam & Ishihama, 1999;Dorman & Deighan, 2003). In Salmonella, NAPs have been shown to influence virulence gene expression (Harrison et al., 1994; O'Byrne & Dorman, 1994a, b; Lucchini et al., 2006;Marshall et al., 1999; Navarre et al., 2006;Schechter et al., 2003). HU binds to DNA relatively non-specifically and influences many DNA-based transactions, including replication, transcription, site-specific-, general and illegitimate recombination, transposition and DNA repair (Kamashev et al., 2008;Li & Waters, 1998;Merickel & Johnson, 2004;Ryan et al., 2002;Semsey et al., 2004;Shanado et al., 1998;Signon & Kleckner, 1995). It also has RNA-binding activity (Balandina et al., 2001) and a preference for binding to unusual conformations in DNA such as four-way junctions and extruded cruciform structures (Kamashev et al., 1999;Pontiggia et al., 1993;Swinger & Rice, 2004).HU is a dimer composed of two closely related subunits, HU a and HU b (Guo & Adhya, 2007) and can exist in three forms, the HU ab heterodimer and the HU a 2 and HU b 2 homodimers. The relative abundances of the three forms vary with the phase of growth (Claret & Rouvière-Yaniv, 1997). The ab heterodimer is the dominant form of the protein at most stages of growth, except at the earliest stage of the exponential phase when the a 2 form predominates; the b 2 homodimer is detectable principally in late stationary phase. The presence of three forms of HU raises the question of w...

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Escherichia coli HU protein suppresses DNA‐gyrase‐mediated illegitimate recombination and SOS induction

Cited by 15 publications

References 33 publications

Translesion DNA polymerases are required for spontaneous deletion formation in Salmonella typhimurium

Translesion DNA polymerases are required for spontaneous deletion formation in Salmonella typhimurium

Quinolone-Mediated Bacterial Death

Nucleoid-associated protein HU controls three regulons that coordinate virulence, response to stress and general physiology in Salmonella enterica serovar Typhimurium

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