Transient Growth Arrest in Escherichia coli Induced by Chromosome Condensation

Conceived and designed the experiments: ABK VVR. Performed the experiments: ALE KSJ. Analyzed the data: ALE KSJ DPS ABK VVR. Wrote the paper: ABK VVR.MukB is a bacterial SMC (structural maintenance of chromosome) protein that regulates the global folding of the Escherichia coli chromosome by bringing distant DNA segments together. We report that moderate overproduction of MukB may lead, depending on strain and growth conditions, to transient growth arrest. In DH5α cells, overproduction of MukB or MukBEF using pBAD expression system triggered growth arrest 2.5 h after induction. The exit from growth arrest was accompanied by the loss of the overproducing plasmid and a decline in the abundance of MukBEF. The arrested cells showed a compound gene expression profile which can be characterized by the following features: (i) a broad and deep downregulation of ribosomal proteins (up to 80-fold); (ii) downregulation of groups of genes encoding enzymes involved in nucleotide metabolism, respiration, and central metabolism; (iii) upregulation of some of the genes responsive to general stress; and (iv) degradation of the patterns of spatial correlations in the transcriptional activity of the chromosome. The transcriptional state of the MukB induced arrest is most similar to stationary cells and cells recovered from stationary phase into a nutrient deprived medium, to amino acid starved cells and to the cells shifting from glucose to acetate. The mukB++ state is dissimilar from all examined transcriptional states generated by protein overexpression with the possible exception of RpoE and RpoH overexpression. Thus, the transcription profile of MukB-arrested cells can be described as a combination of responses typical for other growth-arrested cells and those for overproducers of DNA binding proteins with a particularly deep down-regulation of ribosomal genes.Yeshttp://www.plosone.org/static/editorial#pee

Reduced viability of arrested cells.

<p>DH5α cells harboring the vector (pBAD), pBB10 (A) or pBB03 (B) were grown in M9CA medium up to OD₆₀₀ of 0.2, supplemented with 0.2% glucose (Glu) or 0.2% arabinose (Ara) and tested for colony formation on LB plates containing 0.2% glucose with or without 100 µg/ml ampicillin, as indicated. DH5α(pBB10) and DH5α(pBB03) cells grown with glucose showed no difference in colony formation when plated with or without the drug (data not shown). The average (± S.D.) of two to six separate measurements of colony forming units (CFU) is shown.</p

Blood Protein Markers of Neocortical Amyloid-β Burden: A Candidate Study Using SOMAscan Technology.

Background: Four previously reported studies have tested for association of blood proteins with neocortical amyloid-β burden (NAB). If shown to be robust, these proteins could have utility as a blood test for enrichment in clinical trials of Alzheimer’s disease (AD) therapeutics. Objective: This study aimed to investigate whether previously identified blood proteins also show evidence for association with NAB in serum samples from the Australian Imaging, Biomarker and Lifestyle Flagship Study of Ageing (AIBL). The study considers candidate proteins seen in cohorts other than AIBL and candidates previously discovered in the AIBL cohort. Methods: Our study used the SOMAscan platform for protein quantification in blood serum. Linear and logistic regressions were used to model continuous NAB and dichotomized NAB respectively using single proteins as a predictor. Multiple protein models were built using stepwise regression techniques and support vectors machines. Age and APOE ɛ4 carriage were used as covariates for all analysis. Results: Of the 41 proteins previously reported, 15 AIBL candidates and 20 non-AIBL candidates were available for testing. Of these candidates, pancreatic polypeptide (PPY) and IgM showed a significant association with NAB. Notably, IgM was found to associate with continuous NAB across cognitively normal control subjects. Conclusions: We have further demonstrated the association of PPY and IgM with NAB, despite technical differences between studies. There are several reasons for a lack of significance for the other candidates including platform differences and the use of serum rather than plasma samples. To investigate the possibility of technical differences causing lack of replication, further studies are required

Patterns of gene set activity during MukB induction.

<p>Gene set scores computed using gene expression responses after 2.5(A2), 5 h (A3) and 7.5 h (A4) post MukB induction, were sorted based on similarity of profiles into four clusters. Clusters 1 and 2 (panels A and B) are characterized by lower gene set scores as compared to pre-treatment control, with maximum perturbation during the 5 h time point. Clusters 3 and 4 (panel C and D) represents gene sets which are induced on average during MukB induction. Cluster 3 gene sets show a positive trend with time of induction, whereas cluster 4 sets exhibit a steady decline in set scores with time.</p

The Lomb periodogram of transcriptional activity.

<p>(A) Spatial series of changes in relative transcript abundances at 2.5 h after induction relative to the time zero (right) or repression (left) of MukB were analyzed as described elsewhere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084027#pone.0084027-Jeong1" target="_blank">[29]</a>. The frequencies that cross the 95% confidence level (horizontal line) were defined as significant. (B) Frequency analysis of transcriptional changes during overproduction of RpoE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084027#pone.0084027-Rhodius1" target="_blank">[27]</a> and RpoH <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084027#pone.0084027-Nonaka1" target="_blank">[28]</a> at the longest tested time points, 60 min and 20 min after induction, respectively.</p