Module 374

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Summary

Residual Gene Count Condition Count 1st Q Condition Block * 5th Q Condition Block *
0.57 20 64 NA NA
"* indicates context in which this module was downregulated (1st Q condition block) or upregulated (5th Q condition block) -see "Module Enrichment profile" panel".

Bicluster expression profile

Expression of genes in subset of conditions included in bicluster on left side of red dashed line and out of bicluster on right of red dashed line. Each condition is represented as a boxplot, ordered by their median expression for the bicluster genes (smallest to largest) and colored according to condition blocks.

Boxplot test

Module Enrichment profile

Gene expression profiles across conditions are sorted as on the left and broken into quintiles following the dashed grey lines. Then each quintile is tested for enrichment of each condition by using hypergeometric test. The deviation from zero indicates over-enrichment.

Boxplot test

Conditions

codY knockout

codY knockout

Integration of metabolism and virulence by Clostridium difficile CodY

Series: GSE23192 | Pubmed ID: 20709897 | Type: Expression profiling by array

Summary:CodY, a global regulatory protein that monitors the nutrient sufficiency of the environment by responding to the intracellular levels of GTP and the branched-chain amino acids, was previously shown to be a potent repressor of toxin gene expression in Clostridium difficile during growth in rich medium. In the intestinal tract, such derepression of toxin synthesis may lead to destruction of epithelial cells and the liberation of potential nutrients for the bacterium. CodY is likely to play an important role in regulating overall cellular physiology as well. In this study, DNA microarray analysis and affinity purification of CodY-DNA complexes were used to identify and distinguish the direct and indirect effects of CodY on global gene transcription. A codY null mutation resulted in >4-fold overexpression of 146 genes (organized in 82 apparent transcription units) and underexpression of 19 genes. In addition to the toxin genes, genes for amino acid biosynthesis, nutrient transport, fermentation pathways, membrane components and surface proteins were overexpressed in the codY mutant. Genome-wide analysis identified more than 350 CodY binding regions, many of which are likely to correspond to sites of direct CodY-mediated regulation. About 60% of the CodY-repressed transcription units were associated with binding regions. Several of these genes were confirmed to be direct targets of CodY by gel mobility shift and DNase I footprinting assays.

Overall Design:The experiment was designed to compare gene expression in codY+ and codY mutant strains grown to mid-exponential phase. Three two-color arrays, representing three biological replicates. Each array compares two strains: JIR8094 (pSD21) and JIR9084::pSD21.

Samples: GSM570801, GSM570802, GSM570803

In vivo vs. In vitro

In vivo vs. In vitro

Comparison of the expression profiles of the 630E strain after 8h, 14h and 38h of infection in mouse

Series: GSE43303,GSE43305 | Pubmed ID: 23897605 | Type: Expression profiling by array

Summary:The virulence factors of Clostridium difficile have been studied for many years, but the main in vivo pathogenesis processes of this bacterium has to be investigated. Especially, data on the early mechanisms of C. difficile adaptation to the host is not yet available. The objective of our study was to improve the understanding of the pathogenesis of C. difficile by the analysis of the genome-wide temporal expression of C. difficile genes during the first hours of infection. Three groups of 4 axenic mice each were challenged by vegetative cells of the 630 C. difficile strain, and sacrified at 8, 14, and 38 hours post-infection. Pure prokaryotic RNA was obtained from caecal bacteria. Comparative hybridizations on strain 630 microarrays were done using cDNA issued from an 8-hours in vitro culture as control, with a dye-swap protocol for each sample. Normalisation and statistical analysis of all data were done with different functions of the limma package. The pathogenesis of C. difficile could be seen as a result of the successful metabolic adaptation of the bacteria to its host, contributing to its persistence and multiplication, and the coordinate expression of virulence factors. Analysis of our data enlightened some of these aspects. The results support strongly a two-step infection model, since there is, during the course of infection, a significant increase in the toxins expression contrasting with a decreased expression of most of the putative colonization factors. Several paralogs of the HMW S-layer protein are also down-regulated, some of them could be strong candidates as colonisation factors. Bacterial adaptation to the microenvironment of the host is assessed by the regulation of numerous metabolic pathways, i.e., the upregulation of the ethanolamine catabolic operon or the modulation of several PTS systems. Inactivation of some putative virulence factors identified by this methodology will complete this analysis.

Overall Design:Transcriptional profiling of the C. difficile 630E strain after 8h, 14h or 38h of infection in mouse.; Three-condition experiments: 630E strain 8h, 14h or 38h of infection in mouse vs. 630E strain 8h in culture. 4 biological replicates for each condition in dye swap.

Samples: GSM1060320, GSM1060321, GSM1060322, GSM1060323, GSM1060324, GSM1060325, GSM1060326, GSM1060327, GSM1060328, GSM1060329, GSM1060330, GSM1060331, GSM1060332, GSM1060333, GSM1060334, GSM1060335, GSM1060336, GSM1060337, GSM1060338, GSM1060339, GSM1060340, GSM1060341, GSM1060342, GSM1060343, GSM1060344, GSM1060345, GSM1060346, GSM1060347, GSM1060348, GSM1060349, GSM1060350, GSM1060351

Early infection

Early infection

Transcription profiling of Caco-2 cells and Clostridium difficile during infection

Series: GSE18407 | Pubmed ID: 20521945 | Type: Expression profiling by array

Summary:Clostridium difficile is an anaerobic spore-forming rod-shaped gram-positive bacterium that can infect both humans and animals. Most studies on the pathogenesis of C. difficile have focused on its toxins and their effect on the host cells. Recently, we utilized microarrays to identify conserved and divergent genes associated with virulence in C. difficile isolates from humans and animals. Our data provided the first clue toward a complex mechanism underlying host adaptation and pathogenesis. Microarray technology offers an efficient high-throughput tool to study the transcriptional profiles of pathogens and infected host cells. Transcriptomes of C. difficile after exposure to environmental and antibiotic stresses and those of human epithelial colorectal Caco-2 cells upon TcdA treatment have been analyzed. To our knowledge, there are still no reports on the transcriptomic study of host-pathogen interactions for C. difficile infection (CDI). In vitro analyses of interplay between host and pathogen are essential to unravel the mechanisms of infection and to investigate the host response to infection. We therefore employed microarrays to study both bacterial and human cellular transcriptome kinetics during CDI to Caco-2 cells. Here we present a large-scale analysis of transcriptional profiles to reveal molecular determinants playing a role in C. difficile pathogenesis and the host response. We found that there were 254 and 224 differentially-expressed genes after CDI in C. difficile and Caco-2 cells, respectively. These genes are clustered according to their functional categories and their potential roles in pathogenesis and host response are discussed. Our results will not only increase our understanding on the host-pathogen interaction, but may also provide targets for drug development.

Overall Design:Clostridium difficile: Control vs Infection (time course); mRNA with genomic DNA of tested and reference strains; ; Caco-2 cells: Control vs Infected with Clostridium difficile; Time-course experiments of Caco-2 cells infected with C. difficile for 30, 60 and 120 min

Samples: GSM458943, GSM458942, GSM458941, GSM458940, GSM458939, GSM458938, GSM458937, GSM458936, GSM458935, GSM458934, GSM458933, GSM458932

Rich vs poor diet

Rich vs poor diet

The in vivo responses elicited by Clostridium difficile in response to the gut commensal B. thetaiotaomicron and diet

Series: GSE60751 | Pubmed ID: | Type: Expression profiling by array

Summary:Analysis of Clostridium difficile (Cd) from the cecal contents of germ-free mice or Bacteroides thetaiotaomicron (Bt)-monocolonized mice on a standard, polysaccharide rich diet or polysaccharide deficient diet 5 days after infection. Results identify genes that are involved in the Cd response to diet, in vivo colonization and in interactions with Bt.

Overall Design:In vitro transcriptional profiles of Clostridium difficile obtained from cecal contents of germ-free or Bt-monocolonized mice on a standard, polysaccharide rich or polysaccharide deficient diet. 4 samples/group. 2 control genomic DNA samples for Clostridium difficile and 2 reference genomic DNA samples for Bacteroides thetaiotaomicron; ; Please note that 4 control samples (genomic DNA) were used to determine whether the genomic DNA correctly bound to the probes and thus, were not included in data processing (i.e no processed/normalized data).

Samples: GSM1487085, GSM1487086, GSM1487087, GSM1487088, GSM1487089, GSM1487090, GSM1487092, GSM1487091

fur knockout

fur knockout

Expression analysis of Clostridium difficile wild type and fur (ferric uptake regulator) mutant in high iron.

Series: GSE69218 | Pubmed ID: | Type: Expression profiling by array

Summary:Investigation of whole genome gene expression level changes in a Clostridium difficile fur (ferric uptake regulator) mutant, compared to the wild type strain 630 erm.; The fur mutant analyzed in this study is further described in Ho and Ellermeier (2015) J. Bacteriology

Overall Design:A microarray study using total RNA recovered from three separate wild type cultures of Clostridium difficile 630 erm strain and three separate cultures of a fur mutant strain (ltrA::ermR) were grown in Tryptone-Yeast Extract medium containing 0.25 mM ferric chloride . Each chip measures the expression level of 3,786 of the 3,787 open reading frames of the C. difficile 630 genome with 18 probes (60 oligomers each) for each gene.

Samples: GSM1695516, GSM1695517, GSM1695518, GSM1695519, GSM1695520, GSM1695521, fur.high.11, fur.high.1.1, fur.high.21, fur.high2.1, fur.high.31, fur.high3.1, fur.low.1, fur.low.2, fur.low2, fur.low.3, fur.low3

Commensal vs germ free

Commensal vs germ free

The in vivo responses elicited by Clostridium difficile in response to the gut commensal B. thetaiotaomicron and diet

Series: GSE60751 | Pubmed ID: | Type: Expression profiling by array

Summary:Analysis of Clostridium difficile (Cd) from the cecal contents of germ-free mice or Bacteroides thetaiotaomicron (Bt)-monocolonized mice on a standard, polysaccharide rich diet or polysaccharide deficient diet 5 days after infection. Results identify genes that are involved in the Cd response to diet, in vivo colonization and in interactions with Bt.

Overall Design:In vitro transcriptional profiles of Clostridium difficile obtained from cecal contents of germ-free or Bt-monocolonized mice on a standard, polysaccharide rich or polysaccharide deficient diet. 4 samples/group. 2 control genomic DNA samples for Clostridium difficile and 2 reference genomic DNA samples for Bacteroides thetaiotaomicron; ; Please note that 4 control samples (genomic DNA) were used to determine whether the genomic DNA correctly bound to the probes and thus, were not included in data processing (i.e no processed/normalized data).

Samples: GSM1487081, GSM1487082, GSM1487083, GSM1487084, GSM1487089, GSM1487090, GSM1487091, GSM1487092

Response to oxygen

Response to oxygen

Clostridium difficile response to oxygen

Series: GSE109175 | Pubmed ID: | Type: Expression profiling by array

Summary:C. difficile was grown in either anaerobic conditions or 2% oxygen and gene expression was compared

Overall Design:C. difficile was grown in either anaerobic conditions or 2% oxygen and gene expression was compared. Two conditions were tested with three replicates each (6 samples total)

Samples: GSM2934766, GSM2934767, GSM2934768

Exponential to stationary phase

Exponential to stationary phase

Metabolic reprogramming with the induction of toxin production of Clostridioides difficile during the stationary phase

Series: GSE115054 | Pubmed ID: | Type: Expression profiling by array

Summary:Systems biology approach of Clostridioides difficile to analyze the temporal changes in the intracellular and extracellular metabolme, transcriptome and proteome along the growth curve in casamino acids medium and the connection to toxin production.

Overall Design:Clostridioides difficile 630∆erm (DSM28645) were grown in a casamino acids medium (CDMM) containing 2 g/L glucose. Samples were taken at five time points along the growth curve (exponential growth: 14.5 h of cultivation, transient phase: 17.25 h, stationary phase 1: 19.25 h, stationary phase 2: 24.25 h, stationary phase 3: 29.25 h). The cultivation was performed with four biological replicates. Reference in transcriptomic acid proteomic measurement was the exponential phase samples.

Samples: GSM3164188, GSM3164189, GSM3164190, GSM3164191, GSM3164192, GSM3164193, GSM3164194, GSM3164195, GSM3164196, GSM3164197, GSM3164198, GSM3164199, GSM3164200, GSM3164201, GSM3164202, GSM3164203

Sporulation
Iron limiting condition

Iron limiting condition

Clostridium difficile response to iron limitation

Series: GSE109453 | Pubmed ID: | Type: Expression profiling by array

Summary:C. difficile was grown in BHIS broth or BHIS broth with 75uM dipridyl and gene expression was compared.

Overall Design:Two conditions were tested at three timepoints with three replicates each (18 samples total).

Samples: GSM2943576, GSM2943577, GSM2943578, GSM2943582, GSM2943583, GSM2943584, GSM2943588, GSM2943589, GSM2943590, WT.high.1, WT.high.2, WT.high.3, fur.high.1, fur.high.2, fur.high2, fur.high.3, fur.high3

de novo identified motifs are listed below

Motif 1 Motif 1 e-value Motif 2 Motif 2 e-value
CAGGAGGGTG 0.76 NA NA

This module is predicted to be regulated by the following regulators by using inferelator

Candidate transcriptional regulators for each module were determined with a linear regression based approach (Inferelator) and by evaluating the statistical significance of the overlap (Hypergeometric) between modules and putative TF and alternative sigma factor regulons (CcpA, CodY, Fur, PrdR, SigB, SigD, SigE, SigF, SigG, SigH, SigK, Spo0A) compiled from available literature.

For filtering high confidence influences, we used hypergeometric test adjusted p-value <=0.05 and minimum four genes in the overlap between the module and the TF regulon. The same thresholds were used for evaluating the functional enrichment.

1. Betas: correspond to the average coefficients of the Bayesian regressions between module expression and TF expression profiles. The values indicate the magnitude and direction (activation or repression for positive or negative values, respectively) of each TF-module interaction. 2. Confidence scores: indicate the likelihood of the TF-module interactions.

Default filter: > 0.1 (Absolute Beta)
TF Module Confidence Score Beta

CD630_21430

Transcriptional regulator, HTH-type
 374 0.74 0.4785

This module is predicted to be regulated by the following regulators by using hypergeometric

Candidate transcriptional regulators for each module were determined with a linear regression based approach (Inferelator) and by evaluating the statistical significance of the overlap (Hypergeometric) between modules and putative TF and alternative sigma factor regulons (CcpA, CodY, Fur, PrdR, SigB, SigD, SigE, SigF, SigG, SigH, SigK, Spo0A) compiled from available literature.

For filtering high confidence influences, we used hypergeometric test adjusted p-value <=0.05 and minimum four genes in the overlap between the module and the TF regulon. The same thresholds were used for evaluating the functional enrichment.

Default filter: < 0.05
Default filter: > 4
TF Module Overlap pvalue Adjusted pvalue

CD630_12750

codY
Transcriptional regulator, GTP-sensingpleiotropic repressor
 374 5 0.00 0.03

The module is significantly enriched with genes associated to the indicated functional terms

The enrichment was determined with hypergeometric test using the genome functional annotation compiled by Girinathan et al (2020).

Default filter:<= 0.05
Default filter > 4
Module Pathway Overlap pvalue Adjusted pvalue
374 Histidine Biosynthesis 7 0.000000 0.000000

Genes that are included in this module

* "Gene essentiality is based on TnSeq Data from: Dembek M, Barquist L, Boinett CJ, et al. High-throughput analysis of gene essentiality and sporulation in Clostridium difficile. mBio. 2015;6(2):e02383. Published 2015 Feb 24.doi:10.1128/mBio.02383-14".

Displaying 1 - 20 of 20
Title Short Name Product Function Essentiality * in vivo Essentiality Rich broth Essentiality Expression
CD630_15500 hisB Imidazoleglycerol-phosphate dehydratase
CD630_32690 Putative oligoendopeptidase F, M3B family
CD630_10370 Conserved hypothetical protein
CD630_15530 hisF Imidazole glycerol phosphate synthase subunitHisF IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit.
CD630_15480 hisG ATP phosphoribosyltransferase (ATP-PRTase)(ATP-PRT) Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity.
CD630_10430 sbcC Nuclease SbcCD subunit C
CD630_15520 hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
CD630_32700 Putative magnesium transport ATPase, MgtC/SapBfamily
CD630_15470 hisZ ATP phosphoribosyltransferase regulatory subunit
CD630_15490 hisC Histidinol-phosphate aminotransferase (Imidazoleacetol-phosphate transaminase)
CD630_10410 addA ATP-dependent nuclease subunit A (ATP-dependenthelicase addA) The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination. The AddA nuclease domain is required for chi fragment generation; this subunit has the helicase and 3' -> 5' nuclease activities.
CD630_21430 Transcriptional regulator, HTH-type
CD630_10400 addB ATP-dependent nuclease subunit B (ATP-dependenthelicase addB), Superfamily 1 UvrD-family The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination. The AddB nuclease domain is not required for chi fragment generation; this subunit has 5' -> 3' nuclease activity. Yes
CD630_10380 Putative helicase, superfamily 1, UvrD-family
CD630_10420 sbcD Nuclease SbcCD subunit D SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3'->5' double strand exonuclease that can open hairpins. It also has a 5' single-strand endonuclease activity.
CD630_10390 Conserved hypothetical protein
CD630_15540 hisI Histidine biosynthesis bifunctional protein HisIE[Includes: Phosphoribosyl-AMP cyclohydrolase ;Phosphoribosyl-ATP pyrophosphatase]
CD630_15510 hisH Imidazole glycerol phosphate synthase subunitHisH IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the synthesis of IGP and AICAR. The resulting ammonia molecule is channeled to the active site of HisF.
CD630_21440 Putative membrane protein Probably functions as a manganese efflux pump.
CD630_20020 Transcriptional regulator, HTH-type
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