Antimicrobial Activities of <i>Dictyostelium</i> Differentiation-Inducing Factors and Their Derivatives

At the end of its life cycle, the cellular slime mold Dictyostelium discoideum forms a fruiting body consisting of spores and a multicellular stalk. Originally, the chlorinated alkylphenone differentiation-inducing factors (DIFs) -1 and -3 were isolated as stalk cell inducers in D. discoideum. Later, DIFs and their derivatives were shown to possess several biologic activities including antitumor and anti-Trypanosoma properties. In this study, we examined the antibacterial activities of approximately 30 DIF derivatives by using several bacterial species. Several of the DIF derivatives strongly suppressed the growth of the Gram-positive bacteria Staphylococcus aureus, Bacillus subtilis, and Enterococcus faecalis and Enterococcus faecium, at minimum inhibitory concentrations (MICs) in the sub-micromolar to low-micromolar range. In contrast, none of the DIF derivatives evaluated had any noteworthy effect on the growth of the Gram-negative bacterium Escherichia coli (MIC, &gt;100 &#181;M). Most importantly, several of the DIF derivatives strongly inhibited the growth of methicillin-resistant S. aureus and vancomycin-resistant E. faecalis and E. faecium. Transmission electron microscopy revealed that treatment with DIF derivatives led to the formation of distinct multilayered structures consisting of cell wall or plasma membrane in S. aureus. The present results suggest that DIF derivatives are good lead compounds for developing novel antimicrobials

Computational Promoter Modeling Identifies the Modes of Transcriptional Regulation in Hematopoietic Stem Cells

<div><p>Extrinsic and intrinsic regulators are responsible for the tight control of hematopoietic stem cells (HSCs), which differentiate into all blood cell lineages. To understand the fundamental basis of HSC biology, we focused on differentially expressed genes (DEGs) in long-term and short-term HSCs, which are closely related in terms of cell development but substantially differ in their stem cell capacity. To analyze the transcriptional regulation of the DEGs identified in the novel transcriptome profiles obtained by our RNA-seq analysis, we developed a computational method to model the linear relationship between gene expression and the features of putative regulatory elements. The transcriptional regulation modes characterized here suggest the importance of transcription factors (TFs) that are expressed at steady state or at low levels. Remarkably, we found that 24 differentially expressed TFs targeting 21 putative TF-binding sites contributed significantly to transcriptional regulation. These TFs tended to be modulated by other nondifferentially expressed TFs, suggesting that HSCs can achieve flexible and rapid responses via the control of nondifferentially expressed TFs through a highly complex regulatory network. Our novel transcriptome profiles and new method are powerful tools for studying the mechanistic basis of cell fate decisions.</p></div

Top ten differentially expressed transcription factors.

<p>* fold change.</p>†<p>M: Mansson et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone.0093853-Mansson1" target="_blank">[8]</a>, Fo: Forsberg et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone.0093853-Forsberg2" target="_blank">[6]</a>, Fi: Ficara et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone.0093853-Ficara1" target="_blank">[9]</a>.</p

Alternative regulators potentially important in the presence of dysfunctional TFBSs that are targeted by differentially expressed TFs.

<p>(A) Heat map showing the regression coefficients (RCs) of 129 potentially important TFBSs () that were identified after the removal of the TFBSs in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone-0093853-g004" target="_blank">Figures 4B</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone.0093853.s004" target="_blank">S4</a>. The overall propensity of TFBS activities were not different from those shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone-0093853-g003" target="_blank">Figure 3A</a>. (B) This removal test identified subnetworks that involve alternative TFBSs targeted by differentially expressed TFs. These included GATA-X, Ets, and IRF, which are related to erythroid/megakaryocytic lineage commitment; 6 TFBSs were targeted by 11 TFs in LT-HSCs, and 5 TFBSs were targeted by 8 TFs in ST-HSCs.</p

Overview of computational promoter modeling.

<p>We searched putative TFBSs and mouse TFs from DNA sequences of TSSs, and used these for inferring TF–TF interaction probability and calculating TGASs. We searched the best combination of TFBSs represented by TGASs to predict FPKMs of a gene class in LT- or ST-HSCs by performing 5-fold CVs iteratively.</p

Extensive transcriptome discovery based on the RNA-seq assay.

<p>(A) Our RNA-seq assay discovered over 8200 mRNAs that were not detected in microarray-based studies. (B) RNA quantities relative to those of the housekeeping gene beta-2 microglobulin (<i>B2m</i>) were correlated in qRT-PCR and RNA-seq assays, but variations were also observed in genes that were expressed at low levels. (C) Analysis of gene expression changes detected a transcriptionally active state in ST-HSCs with a larger number of genes than those considered previously. (D) We categorized genes into 4 classes; Class A and Class B, in which FC and FPKM , Class C (6332 genes), in which FC and FPKM , and Class D (6006 genes), in which FPKM . Class A and Class B represented DEGs, Class C represented steady-state transcription genes, and Class D represented genes with noisy expression and/or functional low-expression genes. (E) Enriched GO biological process (GO-BP) terms detected by DAVID (EASE score, , complete lists in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone.0093853.s015" target="_blank">Tables S10</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone.0093853.s016" target="_blank">S11</a>).</p