Identification of the alternative sigma factor regulons of Chlamydia trachomatis using multiplexed CRISPR interference
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ABSTRACT:
PROVIDER: PRJNA962055 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24310800_1.fastq.gz | Fastqsanger.gz | |||
| SRR24310800_2.fastq.gz | Fastqsanger.gz | |||
| SRR24310801_1.fastq.gz | Fastqsanger.gz | |||
| SRR24310801_2.fastq.gz | Fastqsanger.gz | |||
| SRR24310802_1.fastq.gz | Fastqsanger.gz |
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Project description:RNAseq analysis was performed for C. trachomatis serovar L2 after knocking down or overexpressing different sigma factors.
2023-09-05 | GSE230645 | GEO
Project description:Chlamydia trachomatis is a developmentally regulated, obligate intracellular bacterium that encodes three sigma factors: σ66, σ54, and σ28. σ66 is the major sigma factor controlling most transcription initiation during early- and mid-cycle development as the infectious elementary body (EB) transitions to the non-infectious reticulate body (RB) that replicates within an inclusion inside the cell. The roles of the minor sigma factors, σ54 and σ28, have not been well characterized to date; however, there are data to suggest each functions in late-stage development and secondary differentiation as RBs transition to EBs. As the process of secondary differentiation itself is poorly characterized, clarifying the function of these alternative sigma factors by identifying the genes regulated by them will further our understanding of chlamydial differentiation. We hypothesize that σ54 and σ28 have non-redundant and essential functions for initiating late gene transcription thus mediating secondary differentiation in Chlamydia. Here, we demonstrate the necessity of each minor sigma factor in successfully completing the developmental cycle. We have implemented and validated multiplexed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference techniques, novel to the chlamydial field to examine the effects of knocking down each alternative sigma factor individually and simultaneously. In parallel, we also overexpressed each sigma factor. Altering transcript levels for either or both alternative sigma factors resulted in a severe defect in EB production as compared to controls. Furthermore, RNA sequencing identified differentially expressed genes during alternative sigma factor dysregulation, indicating the putative regulons of each. These data demonstrate that the levels of alternative sigma factors must be carefully regulated to facilitate chlamydial growth and differentiation. IMPORTANCE Chlamydia trachomatis is a significant human pathogen in both developed and developing nations. Due to the organism's unique developmental cycle and intracellular niche, basic research has been slow and arduous. However, recent advances in chlamydial genetics have allowed the field to make significant progress in experimentally interrogating the basic physiology of Chlamydia. Broadly speaking, the driving factors of chlamydial development are poorly understood, particularly regarding how the later stages of development are regulated. Here, we employ a novel genetic tool for use in Chlamydia while investigating the effects of dysregulating the two alternative sigma factors in the organism that help control transcription initiation. We provide further evidence for both sigma factors' essential roles in late-stage development and their potential regulons, laying the foundation for deeper experimentation to uncover the molecular pathways involved in chlamydial differentiation.
| S-EPMC10597470 | biostudies-literature
Project description:Staphylococcus aureus has been shown to cause various types of tissue and systemic infections in humans and livestock with the mortality rate of 20-30%. Some isolates can be highly resistant to antibiotics hence the need to identify better drugs and drug targets. Previous studies have shown that (E)-N-(4-Fluorophenyl)-2-phenylethene sulfonamide (FPSS) could inhibit activities of a bacteria-specific transcription factor sigma B. Sigma B regulons in Bacillus subtilis and in Listeria monocytogenes, including virulence factor genes in L. monocytogenes, were decreased. Since sigma B is also presented in S. aureus, we initially postulated the use of FPSS to target S. aureus sigma B activity and to attenuate its virulence gene expression. Surprisingly, qRT-PCR results revealed that FPSS induced expression of sigma B-dependent gene asp23. RNAseq results showed 39 S. aureus genes were affected by FPSS (37 genes were downregulated and two genes were upregulated). FPSS had no effect on expression of sigB operon in S. aureus.
2025-04-21 | GSE253363 | GEO
Project description:The extracytoplasmic function (ECF) σ factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. The emerging pathogen Arcobacter butzleri possesses seven putative pairs of σ/anti-σ factors belonging to the ECF family. Here, we report the identification of the genes regulated by five out of the seven A. butzleri ECF σ factors. Three of the ECF σ factors play an apparent role in transport, energy generation and the maintainance of redox balance. Several genes like the nap, sox and tct genes are regulated by more than one ECF σ factor indicating that the A. butzleri ECF σ factors form a network of overlapping regulons. In contrast to other eubacteria, these A. butzleri ECF regulons appear to primarily regulate responses to changing environments in order to meet metabolic needs instead of an obvious role in stress adaptation.
2011-12-31 | GSE34089 | GEO
Project description:Late gene regulation by the alternative sigma factors of Chlamydia trachomatis [sig28_ChIP-seq]
| PRJNA1249427 | ENA
Project description:Late gene regulation by the alternative sigma factors of Chlamydia trachomatis [sig54_ChIP-seq]
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Project description:Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. Genes regulated by sigma(M) have a characteristic pattern of induction in response to cell envelope-acting antibiotics as evidenced by hierarchical clustering analysis. sigma(M) also contributes to the expression of the Spx transcription factor and thereby indirectly regulates genes of the Spx regulon. Cell envelope stress responses also include regulons controlled by sigma(W), sigma(B) and several two-component regulatory systems (e.g. LiaRS, YycFG, BceRS). Activation of the sigma(M) regulon increases expression of proteins functioning in transcriptional control, cell wall synthesis and shape determination, cell division, DNA damage monitoring, recombinational repair and detoxification.
2008-12-05 | GSE13820 | GEO
Project description:The pathogenic bacterium Chlamydia reproduces via two specialized forms inside a eukaryotic host cell. The dividing form called the reticulate body (RB) must convert at late times into the infectious elementary body (EB) for spread to a new host cell. Late genes are a temporal class of chlamydial genes believed to be responsible for RB-to-EB conversion, but late gene regulation is incompletely understood. In this study, we used chromatin immunoprecipitation (ChIP) to investigate two alternative sigma factors, σ28 and σ54, that alter the promoter specificity of C. trachomatis RNA-polymerase. σ28 ChIP-seq identified hctB and tsp as the only promoters bound by σ28, and binding only occurred late, around the time of RB-to-EB conversion. A σ28 overexpression strain confirmed that these genes are transcribed in a σ28-dependent manner. σ54 ChIP-seq showed that σ54 only bound ctl0021 and ctl0052, and only at late times. This σ54 regulon appears to be conserved as in silico analysis identified σ54 promoter sequences upstream of ctl0021 and ctl0052 homologs in all Chlamydia spp. The genes encoding σ28 and σ54 were only transcribed at late times, but ChIP analysis with the late regulator Euo showed that Euo only controls σ28 expression, and late transcription of σ54 is regulated in an Euo-dependent manner. Thus, multiple mechanisms regulate late genes, including Euo and different forms of RNA polymerase. The dedicated use of two alternative RNA polymerases to control just four late genes suggests that these genes and the independent control of their temporal expression are important for RB-to-EB conversion.
2025-04-30 | GSE294424 | GEO
Project description:The pathogenic bacterium Chlamydia reproduces via two specialized forms inside a eukaryotic host cell. The dividing form called the reticulate body (RB) must convert at late times into the infectious elementary body (EB) for spread to a new host cell. Late genes are a temporal class of chlamydial genes believed to be responsible for RB-to-EB conversion, but late gene regulation is incompletely understood. In this study, we used chromatin immunoprecipitation (ChIP) to investigate two alternative sigma factors, σ28 and σ54, that alter the promoter specificity of C. trachomatis RNA-polymerase. σ28 ChIP-seq identified hctB and tsp as the only promoters bound by σ28, and binding only occurred late, around the time of RB-to-EB conversion. A σ28 overexpression strain confirmed that these genes are transcribed in a σ28-dependent manner. σ54 ChIP-seq showed that σ54 only bound ctl0021 and ctl0052, and only at late times. This σ54 regulon appears to be conserved as in silico analysis identified σ54 promoter sequences upstream of ctl0021 and ctl0052 homologs in all Chlamydia spp. The genes encoding σ28 and σ54 were only transcribed at late times, but ChIP analysis with the late regulator Euo showed that Euo only controls σ28 expression, and late transcription of σ54 is regulated in an Euo-dependent manner. Thus, multiple mechanisms regulate late genes, including Euo and different forms of RNA polymerase. The dedicated use of two alternative RNA polymerases to control just four late genes suggests that these genes and the independent control of their temporal expression are important for RB-to-EB conversion.
2025-04-30 | GSE294423 | GEO
Project description:In this study, we performed a ChIP-chip experiment to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and immuno-precipitated the regions of the genomic DNA interacting with the sigma factors.
2012-08-03 | GSE39711 | GEO