Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide prediction and validation of M-OM-^C70 promoters in Lactobacillus plantarum WCFS1

ABSTRACT: Background: In prokaryotes, sigma factors are essential for the targeting of the transcription machinery to promoters. Various sigma factors have been described that recognize and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor M-OM-^C70 is commonly involved in transcription of the cell's general housekeeping genes, which is mediated by the conserved M-OM-^C70 promoter sequence motifs. This study detects and predicts the general M-OM-^C70-promoter sequences in Lactobacillus plantarum WCFS1 using genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with experimentally detected transcription starts sites (TSSs) using high-resolution tiling array transcriptome datasets. Results: To identify M-OM-^C70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focusing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved M-OM-^C70-promoter consensus. Position weight matrices-based models of the recovered M-OM-^C70-promoter sequence motif were employed to identify 4746 motifs with significant similarity (p-value < 10-4) to the model-motif in the L. plantarum genome. Genome-wide transcription start site information deduced from whole genome tiling-array transcriptome datasets revealed 936 TSSs that were employed to validate the transcriptionally active fraction of these predicted promoters. In total, 578 predicted promoters were found in proximity (M-bM-^IM-$ 100 nucleotides) of the identified TSSs, showing a highly significant co-occurrence of predicted promoter and measured TSS (p-value < 10-23). An additional 224 predicted promoters was validated when the significant similarity to the model-motif was applied less strictly (10-4 M-bM-^IM-$ p-value < 10-3). Conclusions: High-resolution tiling arrays provide a suitable source for TSS detection at a genome-wide level, and allow experimental verification of in silico-predicted promoter sequence motifs. Triplicate hybridizations (technical replicates) of two L. plantarum WCFS1 samples (biological replicates) gathered from a fermentation run at OD600 of 1. Dye swap applied to one of the three technical replicates.

ORGANISM(S): Lactobacillus plantarum WCFS1

SUBMITTER: Michiel Wels

PROVIDER: E-GEOD-36898 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: In prokaryotes, sigma factors are essential for the targeting of the transcription machinery to promoters. Various sigma factors have been described that recognize and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor σ70 is commonly involved in transcription of the cell's general housekeeping genes, which is mediated by the conserved σ70 promoter sequence motifs. This study detects and predicts the general σ70-promoter sequences in Lactobacillus plantarum WCFS1 using genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with experimentally detected transcription starts sites (TSSs) using high-resolution tiling array transcriptome datasets. Results: To identify σ70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focusing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved σ70-promoter consensus. Position weight matrices-based models of the recovered σ70-promoter sequence motif were employed to identify 4746 motifs with significant similarity (p-value < 10-4) to the model-motif in the L. plantarum genome. Genome-wide transcription start site information deduced from whole genome tiling-array transcriptome datasets revealed 936 TSSs that were employed to validate the transcriptionally active fraction of these predicted promoters. In total, 578 predicted promoters were found in proximity (≤ 100 nucleotides) of the identified TSSs, showing a highly significant co-occurrence of predicted promoter and measured TSS (p-value < 10-23). An additional 224 predicted promoters was validated when the significant similarity to the model-motif was applied less strictly (10-4 ≤ p-value < 10-3). Conclusions: High-resolution tiling arrays provide a suitable source for TSS detection at a genome-wide level, and allow experimental verification of in silico-predicted promoter sequence motifs.

Project description:Specific Lactobacillus strains are marketed as probiotics i.e. health promoting organisms. As previously shown in vivo, L. plantarum WCFS1 modulates immune responses via nuclear factor (NF)kB in a growth phase dependent manner, likely caused by changed microbial cell surface characteristics. Here, we identified the differential cell-surface proteome composition of L. plantarum WCFS1 cells derived from the mid-logarithmic and late stationary growth phase by surface trypsination of intact bacterial cells, followed by a combined 1D- and 2D-LC-MS shotgun proteomics strategy, and growth phase dependent transcriptome analysis. Overall, these analyses led to the identification of 31 surface proteins differentially present in the logarithmic and stationary phase, whereas additional 17 and 33 proteins appeared solely present in stationary and logarithmic phase of growth, respectively. From 75% of predicted surface related genes displaying relatively high expression levels, the corresponding proteins were detected, demonstrating a high correlation between transcriptome and proteome profiles. The impact of cell-surface peptide fractions on cellular host responses was evaluated using NFkB promoter activation assays in intestinal epithelial cells, revealing that only late stationary phase derived peptides are capable of attenuating flagellin and cell envelope induced NFkB activation. Overall our data mechanistically expand earlier observations that revealed growth-phase dependent immunomodulation by L. plantarum WCFS1, leading to a typical adjuvant- or tolerance-like response after exposure to stationary phase harvested bacterial cells. Sub-fractionation of the late stationary phase peptide fraction revealed a sub-set of strong attenuator peptides able to manipulate NFkB related pathways to hereby attenuate pro-inflammatory signaling. Samples were hybridizedin a loop design linking each timepoint to the next as well as the previous timepoint. Additional hybridizations were introduced linking each sample three timepoints forward and three timepoints back. All samples were hybridized unsing at least each of the two dyes once.

Project description:Lactobacillus plantarum is a common inhabitant of mammalian gastrointestinal tracts and specific strains belonging to this species are marketed as probiotics intended to confer beneficial health effects. To assist in determining the physiological status and host-microbe interactions of L. plantarum in the digestive tract we assessed changes in the transcriptome of L. plantarum WCFS1 during colonization of the cecum of germ-free mice. According to the transcript profiles L. plantarum WCFS1 was metabolically active and not under severe stress in this intestinal compartment. Carbohydrate metabolism was the most strongly affected functional gene category whereby many genes encoding diverse sugar transport and degradation pathways were induced in mice even compared to L. plantarum grown in a mouse chow-derived laboratory medium. This suggests that the ability of L. plantarum WCFS1 to consume diverse energy sources including plant-associated and host-derived carbohydrates was increased during its residence in the digestive tract. Many of these genes were also induced in L. plantarum colonizing germ-free mice fed a humanized Western-style diet. Similarly a core set of genes encoding cell surface-related properties were differentially expressed in mice. This set includes genes required for the D-alanylation and glycosylation of lipoteichoic acids that were strongly down-regulated in mice. In total L. plantarum exhibits a distinct in vivo transcriptome directed towards adaptation to the mouse intestinal environment. Keywords: cell type comparison Six-week old germ-free C57 Black-6 male mice were inoculated with a single dose of 109 CFU of exponential-phase L. plantarum WCFS1 cells. The mice were sacrificed 15 days later, after sufficient time had passed for several turnovers of the intestinal epithelium and its overlying mucosal layer. Four mice were fed on Chow diet and two mice were fed on western style diet. RNA was isolated from the cecum of these mice. The transcriptome of L. plantarum in these mice was compared to that of L. plantarum grown on MRS broth, Chow broth, or on chemically defined media with either glucose or lactose as carbon- and energy source.

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Genome-wide prediction and validation of M-OM-^C70 promoters in Lactobacillus plantarum WCFS1

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