Additional file 2: Table S1. of Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

A complete list of genes that are differentially expressed in response to nitrogen limitation in M. smegmatis. (XLSX 2413 kb

Additional file 6: Figure S3. of Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

Images of IGV files from differentially expressed intergenic regions and antisense-strand reads mentioned in the text. (PPTX 495 kb

Additional file 5: Table S3. of Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

A list of genes that are differentially expressed in continuous culture, but not in batch culture. (XLSX 89 kb

Additional file 9: Figure S5. of Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

Principal component plot of the samples as calculated from the variance stabilising transformation of the count data using DESeq and heatmap showing the Euclidean distances between the samples from the variance stabilising transformation of the count data using DESeq. (PPTX 72 kb

Additional file 7: Table S4. of Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

A list of differentially expressed intergenic and antisense-strand regions. (XLSX 12 kb

Le Bonhomme mayennais : journal de Lassay, Pré-en-Pail et cantons voisins ["puis" journal de Lassay, Pré-en-Pail, des cantons voisins et du département]...

27 février 18871887/02/27 (A3,N180)-1887/02/27.Appartient à l’ensemble documentaire : BNormand

Additional file 11: Figure S1. of Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b

Weighted Venn diagrams representing overlap of the differential gene expression results from this work with those from stationary phase induction and response to macrophage infection. (PDF 163 kb

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in <i>Mycobacterium tuberculosis</i>

<div><p>The PhoPR two-component system is essential for virulence in <i>Mycobacterium tuberculosis</i> where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in <i>phoP</i> lead to compromised production of pathogen-specific cell wall components and attenuation both <i>ex vivo</i> and <i>in vivo</i>. Using antibodies against the native protein in ChIP-seq experiments (chromatin immunoprecipitation followed by high-throughput sequencing) we demonstrated that PhoP binds to at least 35 loci on the <i>M. tuberculosis</i> genome. The PhoP regulon comprises several transcriptional regulators as well as genes for polyketide synthases and PE/PPE proteins. Integration of ChIP-seq results with high-resolution transcriptomic analysis (RNA-seq) revealed that PhoP controls 30 genes directly, whilst regulatory cascades are responsible for signal amplification and downstream effects through proteins like EspR, which controls Esx1 function, <i>via</i> regulation of the <i>espACD</i> operon. The most prominent site of PhoP regulation was located in the intergenic region between <i>rv2395</i> and <i>PE_PGRS41</i>, where the <i>mcr7</i> gene codes for a small non-coding RNA (ncRNA). Northern blot experiments confirmed the absence of Mcr7 in an <i>M. tuberculosis phoP</i> mutant as well as low-level expression of the ncRNA in <i>M. tuberculosis</i> complex members other than <i>M. tuberculosis</i>. By means of genetic and proteomic analyses we demonstrated that Mcr7 modulates translation of the <i>tatC</i> mRNA thereby impacting the activity of the Twin Arginine Translocation (Tat) protein secretion apparatus. As a result, secretion of the immunodominant Ag85 complex and the beta-lactamase BlaC is affected, among others. Mcr7, the first ncRNA of <i>M. tuberculosis</i> whose function has been established, therefore represents a missing link between the PhoPR two-component system and the downstream functions necessary for successful infection of the host.</p></div

Mapping of PhoP binding sites in the <i>M. tuberculosis</i> chromosome by ChIP-seq.

<p><b>A.</b> UCSC genome browser view showing PhoP binding regions across the <i>M. tuberculosis</i> genome. Peak height correlates with sequence reads and consequently with PhoP binding affinity. The use of a <i>phoP</i> mutant in this experiment (bottom panel) allows identification of false positive signals. <b>B.</b> PhoP and RNA polymerase (RNApol) ChIP-seq profiles for selected genes. Note that the PhoP binding site lies upstream that of RNApol for <i>lipF</i>, <i>narK1</i>, <i>pks2</i> and <i>pks3</i>, known to be transcriptionally activated by PhoP. The position of the PhoP binding region lies downstream that of RNApol for the <i>PE8</i> gene. PhoP binding at the 3′-end of <i>hddA</i> is shown as an example of non-canonical target. <b>C.</b> Bar diagram showing distance (in bp) between the PhoP binding sites and the start codon of adjacent ORFs. <b>D.</b> Bar diagram showing distance between the position of the PhoP binding site and the summit of the RNApol peak calculated from ChIP-seq data. <b>E.</b> Sequence logo showing the consensus sequence derived from the PhoP binding sites identified by ChIP-seq.</p

Summary of ChIP-seq results showing localization of PhoP binding sites in the <i>M. tuberculosis</i> genome.

<p>The table lists regions enriched in immunoprecipitated PhoP-DNA complexes from the H37Rv wild type strain as compared to the <i>phoP</i> mutant. Fold change expression values as determined by RNA-seq experiments are also reported for the flanking genes. Predicted or validated operons found to be deregulated in the <i>phoP</i> mutant are indicated.</p>a<p>p value <0.0001.</p>b<p>FDR 0.00%.</p>c<p>This column lists the predicted operons (according to <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004183#ppat.1004183-Uplekar1" target="_blank">[17]</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004183#ppat.1004183-Roback1" target="_blank">[18]</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004183#ppat.1004183-Price1" target="_blank">[19]</a>), located downstream of PhoP binding sites, that were found to be deregulated in the <i>phoP</i> mutant compared to the wild type strain.</p>§<p>Region detected is between two genes transcribed in opposite direction.</p>£<p>Region located in 3′-end of the gene.</p><p>ND: fold change expression levels of <i>phoP</i> were not quantified since the gene carries a deletion in the mutant strain.</p