Multiple DNA binding proteins contribute to timing of chromosome replication in <i>E. coli</i>

Chromosome replication in Escherichia coli is initiated from a single origin, oriC. Initiation involves a number of DNA binding proteins, but only DnaA is essential and specific for the initiation process. DnaA is an AAA+ protein that binds both ATP and ADP with similar high affinities. DnaA associated with either ATP or ADP binds to a set of strong DnaA binding sites in oriC, whereas only DnaA(ATP) is capable of binding additional and weaker sites to promote initiation. Additional DNA binding proteins act to ensure that initiation occurs timely by affecting either the cellular mass at which DNA replication is initiated, or the time window in which all origins present in a single cell are initiated, i.e. initiation synchrony, or both. Overall, these DNA binding proteins modulate the initiation frequency from oriC by: (i) binding directly to oriC to affect DnaA binding, (ii) altering the DNA topology in or around oriC, (iii) altering the nucleotide bound status of DnaA by interacting with non-coding chromosomal sequences, distant from oriC, that are important for DnaA activity. Thus, although DnaA is the key protein for initiation of replication, other DNA-binding proteins act not only on oriC for modulation of its activity but also at additional regulatory sites to control the nucleotide bound status of DnaA. Here we review the contribution of key DNA binding proteins to the tight regulation of chromosome replication in E. coli cells

Control regions for chromosome replication are conserved with respect to sequence and location among Escherichia coli strains

In Escherichia coli, chromosome replication is initiated from oriC by the DnaA initiator protein associated with ATP. Three non-coding regions contribute to the activity of DnaA. The datA locus is instrumental in conversion of DnaAATP to DnaAADP (DDAH; datA dependent DnaAATP hydrolysis) whereas DnaA rejuvenation sequences 1 and 2 (DARS1 and DARS2) reactivate DnaAADP to DnaAATP. The structural organization of oriC, datA, DARS1 and DARS2 were found conserved between 59 fully sequenced E. coli genomes, with differences primarily in the non-functional spacer regions between key protein binding sites. The relative distances from oriC to datA, DARS1 and DARS2, respectively, was also conserved despite of large variations in genome size, suggesting that the gene dosage of either region is important for bacterial growth. Yet all three regions could be deleted alone or in combination without loss of viability. Competition experiments during balanced growth in rich medium and during mouse colonization indicated roles of datA, DARS1 and DARS2 for bacterial fitness although the relative contribution of each region differed between growth conditions. We suggest that this fitness cost contribute to conservation of both sequence and chromosomal location for datA, DARS1 and DARS2

Oxidative DNA damage is instrumental in hyperreplication stress-induced inviability of Escherichia coli

En Escherichia coli, un aumento en la forma unida de ATP del iniciador de proteína DnaA da resultados en hiperiniciación e inviabilidad. Aquí, mostramos que dicha replicación de estrés es tolerada en el crecimiento anaeróbico. En las células de hiperiniciación, un cambio de la anaeróbica para crecimiento aeróbico dio como resultado la fragmentación aparente de cromosomas y una disminución en su concentración terminal, lo que conduce a un aumento dramático de la ratio ori/ter y el cese del crecimiento celular. La viabilidad aeróbica fue restaurada por reducir el nivel de especies reactivas del oxígeno (ROS) o por eliminación mutM (Fpg glicosilasa). Las roturas de la doble hélice observadas en las células de hiperiniciación resultan, por lo tanto, del encuentro entre los tenedores de replicación y las lesiones de ADN de una sola hélice generadas mientras se quitan bases oxidadas, principalmente 8-oxoG, a partir del ADN. Llegamos a la conclusión de que existe un delicado equilibrio entre la replicación cromosómica y el daño del ADN infligido a ROS por lo que el número de horquillas de replicación sólo puede aumentar cuando la formación de ROS se reduce o si la reparación pertinente se ve comprometida.In Escherichia coli, an increase in the ATP bound form of the DnaA initiator protein results in hyperinitiation and inviability. Here, we show that such replication stress is tolerated during anaerobic growth. In hyperinitiating cells, a shift from anaerobic to aerobic growth resulted in appearance of fragmented chromosomes and a decrease in terminus concentration, leading to a dramatic increase in ori/ter ratio and cessation of cell growth. Aerobic viability was restored by reducing the level of reactive oxygen species (ROS) or by deleting mut M (Fpg glycosylase). The double-strand breaks observed in hyperinitiating cells therefore results from replication forks encountering single-stranded DNA lesions generated while removing oxidized bases, primarily 8-oxoG, from the DNA. We conclude that there is a delicate balance between chromosome replication and ROS inflicted DNA damage so the number of replication forks can only increase when ROS formation is reduced or when the pertinent repair is compromised.-- Unión Europea (PIRG05-GA-2009-247241) -- Danish Research Concil for Natural Sciences (09-064250/FNU) -- Lundbeck Foundation -- Novo Nordist Foundation -- University of Copenhagen para presenter por open accesspeerReviewe

Growth Rate of <i>Escherichia coli</i> During Human Urinary Tract Infection:Implications for Antibiotic Effect

Escherichia coli is the primary cause of urinary tract infection (UTI), which is one of the most frequent human infections. While much is understood about the virulence factors utilized by uropathogenic E. coli (UPEC), less is known about the bacterial growth dynamics taking place during infection. Bacterial growth is considered essential for successful host colonization and infection, and most antibiotics in clinical use depend on active bacterial growth to exert their effect. However, a means to measure the in situ bacterial growth rate during infection has been lacking. Due to faithful coordination between chromosome replication and cell growth and division in E. coli, chromosome replication provides a quantitative measure of the bacterial growth rate. In this study, we explored the potential for inferring in situ bacterial growth rate from a single urine sample in patients with E. coli bacteriuria by differential genome quantification (ori:ter) performed by quantitative PCR. We found active bacterial growth in almost all samples. However, this occurs with day-to-day and inter-patient variability. Our observations indicate that chromosome replication provides not only a robust measure of bacterial growth rate, but it can also be used as a means to evaluate antibiotic effect

Secretion of alpha-hemolysin by<i> Escherichia coil</i> disrupts tight junctions in ulcerative colitis patients

OBJECTIVES: The potential of Escherichia coli (E. coli) isolated from inflammatory bowel disease (IBD) patients to damage the integrity of the intestinal epithelium was investigated. METHODS: E. coli strains isolated from patients with ulcerative colitis (UC) and healthy controls were tested for virulence capacity by molecular techniques and cytotoxic assays and transepithelial electric resistance (TER). E. coliisolate p19A was selected, and deletion mutants were created for alpha-hemolysin (α-hemolysin) (hly) clusters and cytotoxic necrotizing factor type 1 (cnf1). ProbioticE. coliNissle and pathogenicE. coliLF82 were used as controls. RESULTS: E. colistrains from patients with active UC completely disrupted epithelial cell tight junctions shortly after inoculation. These strains belong to phylogenetic group B2 and are all α-hemolysin positive. In contrast, probioticE. coliNissle, pathogenicE. coliLF82, fourE. colifrom patients with inactive UC and threeE. colistrains from healthy controls did not disrupt tight junctions.E. colip19A WT as well ascnf1, and single loci ofhlymutants from cluster I and II were all able to damage Caco-2 (Heterogeneous human epithelial colorectal adenocarcinoma) cell tight junctions. However, this phenotype was lost in a mutant with knockout (Δ) of bothhlyloci (P<0.001). CONCLUSIONS: UC-associated E. coliproducing α-hemolysin can cause rapid loss of tight junction integrity in differentiated Caco-2 cell monolayers. This effect was abolished in a mutant unable to express α-hemolysin. These results suggest that high Hly expression may be a mechanism by which specific strains of E. colipathobionts can contribute to epithelial barrier dysfunction and pathophysiology of disease in IBD

Re-wiring of energy metabolism promotes viability during hyperreplication stress in E. coli

Chromosome replication in Escherichia coli is initiated by DnaA. DnaA binds ATP which is essential for formation of a DnaA-oriC nucleoprotein complex that promotes strand opening, helicase loading and replisome assembly. Following initiation, DnaAATP is converted to DnaAADP primarily by the Regulatory Inactivation of DnaA process (RIDA). In RIDA deficient cells, DnaAATP accumulates leading to uncontrolled initiation of replication and cell death by accumulation of DNA strand breaks. Mutations that suppress RIDA deficiency either dampen overinitiation or permit growth despite overinitiation. We characterize mutations of the last group that have in common that distinct metabolic routes are rewired resulting in the redirection of electron flow towards the cytochrome bd-1. We propose a model where cytochrome bd-1 lowers the formation of reactive oxygen species and hence oxidative damage to the DNA in general. This increases the processivity of replication forks generated by overinitiation to a level that sustains viability