RecA can stimulate the relaxation activity of topoisomerase I: Molecular basis of topoisomerase-mediated genome-wide transcriptional responses in Escherichia coli

Reckinger, Amy R.; Jeong, Kyeong Soo; Khodursky, Arkady B.; Hiasa, Hiroshi

doi:10.1093/nar/gkl981

Cited by 18 publications

(24 citation statements)

References 53 publications

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“…14,15 The alteration of DNA topology in particular, affect not only the duplication of the chromosome but transcription and gene expression. Although it has been reported that certain thermo-sensitive mutations in gyrA or gyrB genes are compensated by the enzyme produced by topA gene and vice versa, [16][17][18][19] the present findings seem to exclude any attenuation or compensatory activity that restore at least in part these functions in the Hfr studied. In particular, growth rate morphological alteration and especially the resistance to nalidixic acid suggest that DNA gyrase enzymes are not working in these bacterial cells.…”

Section: Discussioncontrasting

confidence: 74%

Characterization of high frequency of recombination strains selected by integrative suppression of F’lac in dnaA, gyrA and gyrB temperature sensitive mutants

Debbia¹,

Marchese²

2017

J Biol Res

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Integration of F'lac plasmid into chromosome of both gyrA(Ts) and gyrB(Ts) cells phenotypically suppress the thermosensitive mutations of the DNA gyrase enzymes. As the comparative strains isolated from dnaA(Ts), these high frequency of recombination (Hfr) derivatives were able to transfer chromosomal markers to recipient strains, showed a growth rate of about 60 min, and developed filamentous forms when incubated at the temperature of 43°C. Conversely to dnaA(Ts) Hfr selected isolates, the great majority of Hfr derivative of gyrase mutants resulted resistant to acridine orange and rifampin. Time-kill experiments carried out at the non-permissive temperature also revealed that nalidixic acid has no antibacterial activity on these Hfr strains while derivatives of dnaA(Ts) mutant, as well as the control strain HfrH, were strongly inhibited by this drug. Therefore F plasmid induced duplication of chromosome in the mutants even if the DNA gyrase enzymes are not working. Of a certain interest is that these bacteria exhibit physiological perturbations that affect the main cellular functions, however, they do not appear essential for the survival of the strains.

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Section: Discussioncontrasting

confidence: 74%

Characterization of high frequency of recombination strains selected by integrative suppression of F’lac in dnaA, gyrA and gyrB temperature sensitive mutants

Debbia¹,

Marchese²

2017

J Biol Res

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“…A functional association between E. coli RecA and topoisomerase I have been reported previously (Cunningham et al 1981; Reckinger et al, 2007). More recently, a role of topoisomerase I was observed in E. coli SOS response (Liu et al, 2011; Yang et al, 2015), which prompted us to verify the possibility of a direct physical interaction between these proteins.…”

Section: Resultssupporting

confidence: 58%

“…According to a previous report (Konola et al, 1994), ATP binds to the P-loop of RecA. E. coli RecA undergoes ATP dependent conformational change (Cox, 2003) that could affect its interaction with topoisomerase I (Cunningham et al 1981; Reckinger et al, 2007). We, therefore tested the influence of ATP on the physical interaction between E. coli RecA and topoisomerase I with pull-down reactions in the absence or presence of ATP.…”

Section: Resultsmentioning

confidence: 99%

“…It has an important function in preventing excess negative supercoiling of DNA (Drlica, 1992) which can affect global transcription and result in growth inhibition. According to a previous report, the relaxation activity of E. coli topoisomerase I is stimulated by RecA; suggesting a functional interaction between RecA and topoisomerase I (Reckinger et al, 2007). It remains unclear whether this stimulatory effect is due to direct protein-protein interaction between E. coli RecA and topoisomerase I, or is only due to the effect of E. coli RecA on DNA conformation.…”

Section: Introductionmentioning

confidence: 83%

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Investigating direct interaction between Escherichia coli topoisomerase I and RecA

Banda

Tiwari

Darici

et al. 2016

Gene

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Protein-protein interactions are of special importance in cellular processes, including replication, transcription, recombination, and repair. Escherichia coli topoisomerase I (EcTOP1) is primarily involved in the relaxation of negative DNA supercoiling. E. coli RecA, the key protein for homologous recombination and SOS DNA-damage response, has been shown to stimulate the relaxation activity of EcTOP1. The evidence for their direct protein-protein interaction has not been previously established. We report here the direct physical interaction between E. coli RecA and topoisomerase I. We demonstrated the RecA-topoisomerase I interaction via pull-down assays, and surface plasmon resonance measurements. Molecular docking supports the observation that the interaction involves the topoisomerase I N-terminal domains that form the active site. Our results from pull-down assays showed that ATP, although not required, enhances the RecA-EcTOP1 interaction. We propose that E. coli RecA physically interacts with topoisomerase I to modulate the chromosomal DNA supercoiling.

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“…Even though the possible extent of DNA topological change due to these changes in gene expression has not been investigated, it is noteworthy that DNA gyrase, and its effect on DNA topology, is an effector of gene expression in R. sphaeroides (42) and E. coli (58,62), and it is tempting to speculate on possible effects of PrrA on DNA conformation.…”

Section: Discussionmentioning

confidence: 99%

Role of the Global Transcriptional Regulator PrrA inRhodobacter sphaeroides2.4.1: Combined Transcriptome and Proteome Analysis

et al. 2008

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The PrrBA two-component regulatory system is a major global regulator in Rhodobacter sphaeroides 2.4.1. Here we have compared the transcriptome and proteome profiles of the wild-type (WT) and mutant PrrA2 cells grown anaerobically in the dark with dimethyl sulfoxide as an electron acceptor. Approximately 25% of the genes present in the PrrA2 genome are regulated by PrrA at the transcriptional level, either directly or indirectly, by twofold or more relative to the WT. The genes affected are widespread throughout all COG (cluster of orthologous group) functional categories, with previously unsuspected "metabolic" genes affected in PrrA2 cells. PrrA was found to act as both an activator and a repressor of transcription, with more genes being repressed in the presence of PrrA (9:5 ratio). An analysis of the genes encoding the 1,536 peptides detected through our chromatographic study, which corresponds to 36% coverage of the genome, revealed that approximately 20% of the genes encoding these proteins were positively regulated, whereas approximately 32% were negatively regulated by PrrA, which is in excellent agreement with the percentages obtained for the wholegenome transcriptome profile. In addition, comparison of the transcriptome and proteome mean parameter values for WT and PrrA2 cells showed good qualitative agreement, indicating that transcript regulation paralleled the corresponding protein abundance, although not one for one. The microarray analysis was validated by direct mRNA measurement of randomly selected genes that were both positively and negatively regulated. lacZ transcriptional and kan translational fusions enabled us to map putative PrrA binding sites and revealed potential gene targets for indirect regulation by PrrA.Rhodobacter sphaeroides 2.4.1 is a purple nonsulfur photosynthetic bacterium which is well studied for its remarkable metabolic versatility. It can grow aerobically, anaerobically in the presence of external electron acceptors, such as dimethyl sulfoxide (DMSO), photosynthetically in the light, and fermentatively and lithotrophically in the presence or absence of oxygen (72). As a reflection of its metabolic versatility, R. sphaeroides has a branched electron transport chain (ETC) that utilizes several terminal respiratory pathways. The expression of genes encoding components of these pathways is coordinately regulated, depending on the prevailing redox conditions and the terminal electron acceptor present.The concentration of oxygen, when used as a terminal electron acceptor, regulates membrane biogenesis in R. sphaeroides; below approximately 3% oxygen, the intracytoplasmic membrane is synthesized (34). This organelle houses components necessary for the photosynthetic lifestyle, such as the various photosystems and electron carriers. In addition to O 2 , incident light intensity also regulates intracytoplasmic membrane abundance and composition in the absence of oxygen.Gene expression in R. sphaeroides is controlled by several well-defined regulatory elements. The expression of th...

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RecA can stimulate the relaxation activity of topoisomerase I: Molecular basis of topoisomerase-mediated genome-wide transcriptional responses in Escherichia coli

Cited by 18 publications

References 53 publications

Characterization of high frequency of recombination strains selected by integrative suppression of F’lac in dnaA, gyrA and gyrB temperature sensitive mutants

Characterization of high frequency of recombination strains selected by integrative suppression of F’lac in dnaA, gyrA and gyrB temperature sensitive mutants

Investigating direct interaction between Escherichia coli topoisomerase I and RecA

Role of the Global Transcriptional Regulator PrrA inRhodobacter sphaeroides2.4.1: Combined Transcriptome and Proteome Analysis

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