Differences in the degree of inhibition of NDP reductase by chemical inactivation and by the thermosensitive mutation nrdA101 in Escherichia coli suggest an effect on chromosome segregation

Tuning the replication fork progression by the initiation frequency

The thermo-resistant period of the thermo-sensitive ribonucleotide reductase RNR101 encoded by the nrdA101 allele in Escherichia coli is prolonged for 50 min at 42°C, enabling an increase in DNA content of about 45%. Assuming that fork progression in the nrdA101 mutant is impaired, the question whether reduced number of ongoing replication rounds altered the thermo-resistant period in this strain was investigated. Decreases in the oriC/terC ratio and in the number of oriC per cell at 30°C were found in the presence of oriC228, oriC229 and oriC239 alleles in strain nrdA101. Correlated with this effect, increased thermo-resistance period of the RNR101 was allowed, and the detrimental effects on cell division, chromosome segregation and cell viability observed in the nrdA101 mutant at 42°C were suppressed. These results indicate that conditions leading to chromosome initiation deficiency at 30°C enhance the replication fork progression in the nrdA101 mutant at 42°C. We propose that coordination between initiation frequency and replication fork progression could be significant for most of the replication systems with important consequences in their cell cycle regulation.

RecA-dependent replication in the nrdA101(Ts) mutant of Escherichia coli under restrictive conditions

Cells carrying the thermosensitive nrdA101 allele are able to replicate entire chromosomes at 42°C when new DNA initiation events are inhibited. We investigated the role of the recombination enzymes on the progression of the DNA replication forks in the nrdA101 mutant at 42°C in the presence of rifampin. Using pulsed-field gel electrophoresis (PFGE), we demonstrated that the replication forks stalled and reversed during the replication progression under this restrictive condition. DNA labeling and flow cytometry experiments supported this finding as the deleterious effects found in the RecB-deficient background were suppressed specifically by the absence of RuvABC; however, this did not occur in a RecG-deficient background. Furthermore, we show that the RecA protein is absolutely required for DNA replication in the nrdA101 mutant at restrictive temperature when the replication forks are reversed. The detrimental effect of the recA deletion is not related to the chromosomal degradation caused by the absence of RecA. The inhibition of DNA replication observed in the nrdA101 recA mutant at 42°C in the presence of rifampin was reverted by the presence of the wild-type RecA protein expressed ectopically but only partially suppressed by the RecA protein with an S25P mutation [RecA(S25P)], deficient in the rescue of the stalled replication forks. We propose that RecA is required to maintain the integrity of the reversed forks in the nrdA101 mutant under certain restrictive conditions, supporting the relationship between DNA replication and recombination enzymes through the stabilization and repair of the stalled replication forks.

Overlap of replication rounds disturbs the progression of replicating forks in a ribonucleotide reductase mutant of Escherichia coli

Ribonucleotide reductase (RNR) is the only enzyme specifically required for the synthesis of deoxyribonucleotides (dNTPs). Surprisingly, Escherichia coli cells carrying the nrdA101 allele, which codes for a thermosensitive RNR101, are able to replicate entire chromosomes at 42 °C under RNA or protein synthesis inhibition. Here we show that the RNR101 protein is unstable at 42 °C and that its degradation under restrictive conditions is prevented by the presence of rifampicin. Nevertheless, the mere stability of the RNR protein at 42 °C cannot explain the completion of chromosomal DNA replication in the nrdA101 mutant. We found that inactivation of the DnaA protein by using several dnaAts alleles allows complete chromosome replication in the absence of rifampicin and suppresses the nucleoid segregation and cell division defects observed in the nrdA101 mutant at 42 °C. As both inactivation of the DnaA protein and inhibition of RNA synthesis block the occurrence of new DNA initiations, the consequent decrease in the number of forks per chromosome could be related to those effects. In support of this notion, we found that avoiding multifork replication rounds by the presence of moderate extra copies of datA sequence increases the relative amount of DNA synthesis of the nrdA101 mutant at 42 °C. We propose that a lower replication fork density results in an improvement of the progression of DNA replication, allowing replication of the entire chromosome at the restrictive temperature. The mechanism related to this effect is also discussed.

Correlation between ribonucleoside-diphosphate reductase and three replication proteins in Escherichia coli

Background

There has long been evidence supporting the idea that RNR and the dNTP-synthesizing complex must be closely linked to the replication complex or replisome. We contributed to this body of evidence in proposing the hypothesis of the replication hyperstructure. A recently published work called this postulate into question, reporting that NrdB is evenly distributed throughout the cytoplasm. Consequently we were interested in the localization of RNR protein and its relationship with other replication proteins.

Results

We tagged NrdB protein with 3×FLAG epitope and detected its subcellular location by immunofluorescence microscopy. We found that this protein is located in nucleoid-associated clusters, that the number of foci correlates with the number of replication forks at any cell age, and that after the replication process ends the number of cells containing NrdB foci decreases.

We show that the number of NrdB foci is very similar to the number of SeqA, DnaB, and DnaX foci, both in the whole culture and in different cell cycle periods. In addition, interfoci distances between NrdB and three replication proteins are similar to the distances between two replication protein foci.

Conclusions

NrdB is present in nucleoid-associated clusters during the replication period. These clusters disappear after replication ends. The number of these clusters is closely related to the number of replication forks and the number of three replication protein clusters in any cell cycle period. Therefore we conclude that NrdB protein, and most likely RNR protein, is closely linked to the replication proteins or replisome at the replication fork. These results clearly support the replication hyperstructure model.

Pseudomonas aeruginosa, under DNA replication inhibition, tends to form biofilms via Arr

Bacteria infecting eukaryotic hosts often encounter therapeutic antimicrobial and DNA damaging agents and respond by forming biofilms. While mechanisms of biofilm response are incompletely understood, they seem to involve bacterial second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) signaling. We hypothesized that DNA replication inhibition induces bacterial biofilm formation via c-di-GMP signaling. Evidently, we found that Pseudomonas aeruginosa mounted a biofilm response to the subinhibitory DNA replication inhibitors hydroxyurea and nalidixic acid, but planktonic proliferation was inhibited. The biofilm response was suppressed either genetically by mutations causing planktonic resistance or biochemically by reversal of replication inhibition. Biofilms were induced by a mechanism of stimulated adhesion of planktonic filaments having impaired DNA replication, as examined under fluorescence microscopy. Induction was suppressed by either inhibition or mutation of Arr-a c-di-GMP phosphodiesterase. These results suggest that P. aeruginosa, under DNA replication stress, tends to form biofilms via Arr. The profound implications of the SOS response, planktonic-sessile and bacteria-cancer relationships are discussed.

Toward a hyperstructure taxonomy

Bacterial cells contain many large, spatially extended assemblies of ions, molecules, and macromolecules, called hyperstructures, that are implicated in functions that range from DNA replication and cell division to chemotaxis and secretion. Interactions between these hyperstructures would create a level of organization intermediate between macromolecules and the cell itself. To explore this level, a taxonomy is needed. Here, we describe classification criteria based on the form of the hyperstructure and on the processes responsible for this form. These processes include those dependent on coupled transcription-translation, protein-protein affinities, chromosome site-binding by protein, and membrane structures. Various combinations of processes determine the formation, maturation, and demise of many hyperstructures that therefore follow a trajectory within the space of classification by form/process. Hence a taxonomy by trajectory may be desirable. Finally, we suggest that working toward a taxonomy based on speculative interactions between hyperstructures promises most insight into life at this level.

Functional taxonomy of bacterial hyperstructures

The levels of organization that exist in bacteria extend from macromolecules to populations. Evidence that there is also a level of organization intermediate between the macromolecule and the bacterial cell is accumulating. This is the level of hyperstructures. Here, we review a variety of spatially extended structures, complexes, and assemblies that might be termed hyperstructures. These include ribosomal or "nucleolar" hyperstructures; transertion hyperstructures; putative phosphotransferase system and glycolytic hyperstructures; chemosignaling and flagellar hyperstructures; DNA repair hyperstructures; cytoskeletal hyperstructures based on EF-Tu, FtsZ, and MreB; and cell cycle hyperstructures responsible for DNA replication, sequestration of newly replicated origins, segregation, compaction, and division. We propose principles for classifying these hyperstructures and finally illustrate how thinking in terms of hyperstructures may lead to a different vision of the bacterial cell.