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RpoE-dependent transcriptomes of Haemophilus ducreyi

ABSTRACT: To potentially understand how H. ducreyi responds to membrane stress, here we defined RpoE-dependent genes using RNA-Seq. We identified 180 RpoE-dependent genes, of which 98% were upregulated; a major set of these genes encodes homologues of envelope maintenance and repair factors. We also identified and validated a putative RpoE promoter consensus sequence, which was enriched in the majority of RpoE-dependent targets. Comparison of RpoE-dependent genes to those controlled by CpxR showed that each transcription factor regulated a distinct set of genes. Given that RpoE activated a large number of genes encoding envelope maintenance and repair factors and CpxRA represses genes encoding envelope-localized proteins, these data suggest that RpoE and CpxRA appear to play distinct yet complementary roles in regulating envelope homeostasis in H. ducreyi.

ORGANISM(S): [Haemophilus] ducreyi

PROVIDER: GSE75238 | GEO | 2015/11/21

SECONDARY ACCESSION(S): PRJNA302860

REPOSITORIES: GEO

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RpoE-dependent transcriptomes of Haemophilus ducreyi

Project description:To potentially understand how H. ducreyi responds to membrane stress, here we defined RpoE-dependent genes using RNA-Seq. We identified 180 RpoE-dependent genes, of which 98% were upregulated; a major set of these genes encodes homologues of envelope maintenance and repair factors. We also identified and validated a putative RpoE promoter consensus sequence, which was enriched in the majority of RpoE-dependent targets. Comparison of RpoE-dependent genes to those controlled by CpxR showed that each transcription factor regulated a distinct set of genes. Given that RpoE activated a large number of genes encoding envelope maintenance and repair factors and CpxRA represses genes encoding envelope-localized proteins, these data suggest that RpoE and CpxRA appear to play distinct yet complementary roles in regulating envelope homeostasis in H. ducreyi. RNA of Haemophilus ducreyi 35000HP wild-type strain containing a rpoE inducible plasmid and wild-type strain containing a control plasmid were collected at 0 minutes, 5 minutes, and 10 minutes after induction in quadruplicate.

2015-11-21 | E-GEOD-75238 | biostudies-arrayexpress

Global gene expression profile of Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88

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Transcriptomes of 35000HP, ΔcpxA, ΔcpxR mutant strains of Haemophilus ducreyi in mid-log, transition, and stationary phase

Project description:To better understand the role of H. ducreyi CpxRA in controlling virulence determinants, here we defined genes potentially regulated by CpxRA by using RNA-Seq. Activation of CpxR by deletion of cpxA repressed nearly 70% of its targets, including seven established virulence determinants. Inactivation of CpxR by deletion of cpxR differentially regulated few genes and increased the expression of one virulence determinant. We identified a CpxR binding motif that was enriched in downregulated but not upregulated targets. These data reinforce the hypothesis that CpxA phosphatase activity plays a critical role in controlling H. ducreyi virulence in vivo. Characterization of the downregulated genes may offer new insights into pathogenesis.

2015-11-21 | GSE75237 | GEO

Transcriptomes of 35000HP, ÎcpxA, ÎcpxR mutant strains of Haemophilus ducreyi in mid-log, transition, and stationary phase

2015-11-21 | E-GEOD-75237 | biostudies-arrayexpress

Global gene expression profile of Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88

Project description:Haemophilus ducreyi 35000HPcpxRpML125 which over-expresses CpxR in a CpxR deletion background, was compared to it vector alone counterpart (35000HPcpxRpLS88) in hopes to elucidate members of the CpxRA regulon. Haemophilus ducreyi 35000HPcpxRpML125 and 35000HPcpxRpLS88 were grown in Columbia broth. After 8 hr of growth, total RNA was isolated and processed for DNA microarray analysis. This study includes 3 biological replicates (paired samples), two of which were selected for dye swap.

2011-05-03 | E-GEOD-21789 | biostudies-arrayexpress

[Haemophilus] ducreyi

Project description:RpoE-dependent transcriptomes of Haemophilus ducreyi

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Transcriptomes of FA1090,, FA1090cpxA::kan, FA1090cpxR::erm mutant strains of Neisseria gonorrhoeae in late log phase

Project description:To better understand the role of Neisseria gonorrhoeae CpxRA in controlling virulence determinants, here we defined genes potentially regulated by CpxRA by using RNA-Seq. We identified approximately 139 genes differentially expressed between cpxA (Cpx system active) and cpxR (Cpx system inactive) mutants. A large number of the differentially expressed genes encode envelope-localized proteins.

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RpoE regulon in Rhodobacter sphaeroides

Project description:In Rhodobacter sphaeroides a transcriptional response to the reactive oxygen species singlet oxygen is controlled by the group IV sigma factor RpoE and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the singlet oxygen stress response that contain RpoE-dependent promoters within R. sphaeroides. Transcript pattern clustering and a RpoE-binding sequence model were used to predict candidate promoters that respond to singlet oxygen stress in R. sphaeroides. These candidate promoters were experimentally validated to nine R. sphaeroides RpoE-dependent promoters that control the transcription of 15 genes activated by singlet oxygen.

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RpoE regulon in Rhodobacter sphaeroides

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The CpxRA two-component system promotes intracellular survival and is a key regulator of virulence factors in Legionella pneumophila

Project description:The bacterium Legionella pneumophila is capable of intracellular replication within freshwater protozoa as well as human alveolar macrophages, the latter of which results in the serious pneumonia Legionnaires’ disease. A primary factor involved in these host cell interactions is the Dot/Icm Type IV secretion system that is responsible for translocating effector proteins needed to establish and maintain the bacterial replicative niche. Several regulatory factors have been identified to control the expression of the Dot/Icm system and effectors, one of which is the CpxRA two-component system, suggesting essentiality for virulence. However, studies elsewhere have shown that L. pneumophila strains harboring mutated cpxRA genes have minimal to no impact on L. pneumophila intracellular growth in protozoa and macrophages. In this study, we generated L. pneumophila cpxR, cpxA, and cpxRA in-frame null mutant strains to further delineate the role of the CpxRA system in bacterial survival and virulence. Surprisingly, we found that cpxR and cpxRA are essential for intracellular replication within Acanthamoeba castellanii, but not in U937 macrophage-like cells. Transcriptome analysis revealed that CpxRA regulates a large number of virulence-associated proteins including a number of Dot/Icm effectors as well as 14 Type II secreted substrates. Furthermore, the cpxR and cpxRA mutants were more sodium resistant than wildtype, and cpxRA expression reaches maximal levels during post-exponential phase. Taken together, our findings suggest the CpxRA system is a key contributor to L. pneumophila virulence via virulence factor regulation.

2016-09-16 | GSE73873 | GEO

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