The Stringent Response Inhibits DNA Replication Initiation in E. coli by Modulating Supercoiling of oriC.

The stringent response enables bacteria to respond to a variety of environmental stresses, especially various forms of nutrient limitation. During the stringent response, the cell produces large quantities of the nucleotide alarmone ppGpp, which modulates many aspects of cell physiology, including reprogramming transcription, blocking protein translation, and inhibiting new rounds of DNA replication. The mechanism by which ppGpp inhibits DNA replication initiation in Escherichia coli remains unclear. Prior work suggested that ppGpp blocks new rounds of replication by inhibiting transcription of the essential initiation factor dnaA, but we found that replication is still inhibited by ppGpp in cells ectopically producing DnaA. Instead, we provide evidence that a global reduction of transcription by ppGpp prevents replication initiation by modulating the supercoiling state of the origin of replication, oriC Active transcription normally introduces negative supercoils into oriC to help promote replication initiation, so the accumulation of ppGpp reduces initiation potential at oriC by reducing transcription. We find that maintaining transcription near oriC, either by expressing a ppGpp-blind RNA polymerase mutant or by inducing transcription from a ppGpp-insensitive promoter, can strongly bypass the inhibition of replication by ppGpp. Additionally, we show that increasing global negative supercoiling by inhibiting topoisomerase I or by deleting the nucleoid-associated protein gene seqA also relieves inhibition. We propose a model, potentially conserved across proteobacteria, in which ppGpp indirectly creates an unfavorable energy landscape for initiation by limiting the introduction of negative supercoils into oriCIMPORTANCE To survive bouts of starvation, cells must inhibit DNA replication. In bacteria, starvation triggers production of a signaling molecule called ppGpp (guanosine tetraphosphate) that helps reprogram cellular physiology, including inhibiting new rounds of DNA replication. While ppGpp has been known to block replication initiation in Escherichia coli for decades, the mechanism responsible was unknown. Early work suggested that ppGpp drives a decrease in levels of the replication initiator protein DnaA. However, we found that this decrease is not necessary to block replication initiation. Instead, we demonstrate that ppGpp leads to a change in DNA topology that prevents initiation. ppGpp is known to inhibit bulk transcription, which normally introduces negative supercoils into the chromosome, and negative supercoils near the origin of replication help drive its unwinding, leading to replication initiation. Thus, the accumulation of ppGpp prevents replication initiation by blocking the introduction of initiation-promoting negative supercoils. This mechanism is likely conserved throughout proteobacteria.

A bacteriophage tubulin harnesses dynamic instability to center DNA in infected cells.

Dynamic instability, polarity, and spatiotemporal organization are hallmarks of the microtubule cytoskeleton that allow formation of complex structures such as the eukaryotic spindle. No similar structure has been identified in prokaryotes. The bacteriophage-encoded tubulin PhuZ is required to position DNA at mid-cell, without which infectivity is compromised. Here, we show that PhuZ filaments, like microtubules, stochastically switch from growing in a distinctly polar manner to catastrophic depolymerization (dynamic instability) both in vitro and in vivo. One end of each PhuZ filament is stably anchored near the cell pole to form a spindle-like array that orients the growing ends toward the phage nucleoid so as to position it near mid-cell. Our results demonstrate how a bacteriophage can harness the properties of a tubulin-like cytoskeleton for efficient propagation. This represents the first identification of a prokaryotic tubulin with the dynamic instability of microtubules and the ability to form a simplified bipolar spindle.

The structure and assembly mechanism of a novel three-stranded tubulin filament that centers phage DNA.

Tubulins are a universally conserved protein superfamily that carry out diverse biological roles by assembling filaments with very different architectures. The underlying basis of this structural diversity is poorly understood. Here, we determine a 7.1 Å cryo-electron microscopy reconstruction of the bacteriophage-encoded PhuZ filament and provide molecular-level insight into its cooperative assembly mechanism. The PhuZ family of tubulins is required to actively center the phage within infected host cells, facilitating efficient phage replication. Our reconstruction and derived model reveal the first example of a three-stranded tubulin filament. We show that the elongated C-terminal tail simultaneously stabilizes both longitudinal and lateral interactions, which in turn define filament architecture. Identified interaction surfaces are conserved within the PhuZ family, and their mutagenesis compromises polymerization in vitro and in vivo. Combining kinetic modeling of PhuZ filament assembly and structural data, we suggest a common filament structure and assembly mechanism for the PhuZ family of tubulins.

Shaping the Future of Research: a perspective from junior scientists.

The landscape of scientific research and funding is in flux as a result of tight budgets, evolving models of both publishing and evaluation, and questions about training and workforce stability. As future leaders, junior scientists are uniquely poised to shape the culture and practice of science in response to these challenges. A group of postdocs in the Boston area who are invested in improving the scientific endeavor, planned a symposium held on October 2 (nd) and 3 (rd), 2014, as a way to join the discussion about the future of US biomedical research. Here we present a report of the proceedings of participant-driven workshops and the organizers' synthesis of the outcomes.

A phage tubulin assembles dynamic filaments by an atypical mechanism to center viral DNA within the host cell.

Tubulins are essential for the reproduction of many eukaryotic viruses, but historically, bacteriophage were assumed not to require a cytoskeleton. Here, we identify a tubulin-like protein, PhuZ, from bacteriophage 201φ2-1 and show that it forms filaments in vivo and in vitro. The PhuZ structure has a conserved tubulin fold, with an unusual, extended C terminus that we demonstrate to be critical for polymerization in vitro and in vivo. Longitudinal packing in the crystal lattice mimics packing observed by EM of in-vitro-formed filaments, indicating how interactions between the C terminus and the following monomer drive polymerization. PhuZ forms a filamentous array that is required for positioning phage DNA within the bacterial cell. Correct positioning to the cell center and optimal phage reproduction only occur when the PhuZ filament is dynamic. Thus, we show that PhuZ assembles a spindle-like array that functions analogously to the microtubule-based spindles of eukaryotes.

Burden of dysthymia and comorbid illness in adults in a Canadian primary care setting: high rates of psychiatric illness in the offspring.

BACKGROUND: The burden of comorbid dysthymia and other comorbid psychiatric illnesses in a Canadian primary care setting was measured. Two groups of primary care patients: those who scored positive for comorbid dysthymia versus those who scored negative for any psychiatric disorder were compared. METHODS: This was a cross-sectional survey in a Health Service Organization (HSO) in Ontario, Canada. The subjects were patients of the HSO. The main outcome measures were: health status, mood, social adjustment, coping ability, children's psychiatric disorders, child development, family function, and health and social service utilization. RESULTS: Of the 6280 eligible adults who were patients at the HSO, 68.9% consented to be screened for psychiatric disorders; 5.1% screened positive for dysthymia, of which 90% had at least one comorbid psychiatric disorder. The following statistically significant differences were found between people with dysthymia and other comorbid psychiatric disorders versus people without any psychiatric disorder. People with dysthymia were more likely to have worse health status, worry more about their health, and report levels of pain that impaired their function; they had higher MADRS depression scores, lower social role function scores, lower social adjustment scores, and lower coping ability. More children of people with comorbid dysthymia met criteria for one or more childhood psychiatric disorders and there were more families with a parent with dysthymia that were dysfunctional. People with dysthymia used a greater proportion of health and social services, had higher per person annual health care costs (excluding hospital services), and had higher per person annual indirect costs (lost wages). CONCLUSION: This analysis demonstrated the burden of illness and costs that this disorder imposes on individuals, their families, and society as a whole.

Sertraline and/or interpersonal psychotherapy for patients with dysthymic disorder in primary care: 6-month comparison with longitudinal 2-year follow-up of effectiveness and costs.

BACKGROUND: There is little information on the long-term effects and costs of a combination of Sertraline and interpersonal psychotherapy (IPT) for the treatment of dysthymia in primary care. METHODS: In a single-blind, randomized clinical trial, 707 adults (18-74 years of age inclusive) with DSM-IV dysthymic disorder, with or without past and/or current major depression, as an acute or chronic episode, in a community-based primary care practice in Ontario, Canada, were randomized to treatment with either Sertraline alone (50-200 mg), or IPT alone (10 sessions), or Sertraline plus IPT combined. In the acute treatment phase (first 6 months) all groups received full active treatment. This was followed by an additional 18-month naturalistic follow-up phase. Subjects were assessed for effectiveness of treatment in reducing depressive symptoms using the Montgomery Asberg Depression Rating Scale (MADRS) at 6 months and twice again during the 18-month follow-up by blind independent observers. Treatment costs and subjects' use of other health and social services were also investigated. RESULTS: At 6 months, 586 subjects completed the MADRS questionnaire. There was a significant difference (P=0.025) in mean MADRS scores: 14.3 (Group I); 14.9 (Group II); 16.8 (Group III), using analysis of covariance. Response (40% improvement) rates were 60.2% for Sertraline alone, 46.6% for IPT alone, and 57.5% for Sertraline augmented by IPT (P=0.02). At 2 years, 525 subjects were retained for follow-up. There was no statistically significant difference between Sertraline alone and Sertraline plus IPT in symptom reduction. However, both were more effective than IPT alone in reducing depressive symptoms (P=0.03). There was a statistically significant difference between groups in costs for use of health and social services. The IPT treatment groups had the lower costs for use of health and social services. CONCLUSIONS: Sertraline or Sertraline plus IPT was more effective than IPT alone after 6 months. Over the long term (2 years), all three treatments provide reasonably effective treatment for reducing symptoms of dysthymia, but Sertraline or combining Sertraline with IPT is more effective than IPT alone. Of these two more effective treatments, subjects in the Sertraline plus IPT group had less health and social service costs by $480 per person over 2 years. These findings underscore the effects of combining pharmacotherapy and psychotherapy and the economic value of this more comprehensive treatment of dysthymia in primary care.