Sigma 28-dependent small RNAs regulate timing of flagella biosynthesis
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PROVIDER: PRJNA730033 | ENA |
REPOSITORIES: ENA
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Project description:Synthesis of flagella is very energy intensive and, while extensive transcriptional regulation has been described, little is known about the post-transcriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators; most base pairing with mRNAs to affect their stability and/or translation. Here we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor, sigma 28 in Escherichia coli. UhpU, MotR and FliX have distinct impacts on flagellin levels, flagella number and swimming, with MotR accelerating flagella synthesis and FliX decelerating flagella synthesis. Interestingly, MotR and FliX are noncanonical in that they base pair within the coding sequences of target genes. We characterize their respective positive and negative effects on genes encoding ribosomal proteins.
2023-09-26 | GSE174487 | GEO
Project description:Flagella are important for bacterial motility as well as for pathogenesis. Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators, most base pairing with mRNAs to affect their stability and/or translation. Here, we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor σ28 (fliA) in Escherichia coli. Interestingly, the four sRNAs have varied effects on flagellin protein levels, flagella number and cell motility. UhpU, corresponding to the 3´ UTR of a metabolic gene, likely has hundreds of targets including a transcriptional regulator at the top flagella regulatory cascade connecting metabolism and flagella synthesis. Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs and act on ribosomal protein mRNAs connecting ribosome production and flagella synthesis. The study shows how sRNA-mediated regulation can overlay a complex network enabling nuanced control of flagella synthesis.
| S-EPMC10578931 | biostudies-literature
Project description:Campylobacter jejuni produces a single flagellum on one or both poles of the cell, the polar flagella not only confer the bacterium darting motility but also involved in its virulence and metabolic processes. FlhF is a lately defined flagella biosynthesis regulator, but how it regulates flagella assembly isn’t clear at present. Previous research had indicated FlhF was associated with gene expression, to understanding its role in flagella system and its correlation with C. jejuni virulence, the global gene expression profiles of C. jejuni NCTC 11168 after inactivation of FlhF was analyzed. Transcriptome analysis revealed that ten genes were significantly differentially expressed with 6 down-regulated and 4 up-regulated, these genes are involved in diverse cellular functions including bacterial chemotaxis, flagellar assembly and two-component system, significance analysis revealed that the pathway of flagellar assembly was remarkable affected. Further studies were focused on the flagella system, FlhF was found play a global role as 63% (41/65) of the flagella genes were down-regulated, it influences flagella gene transcription from the early stage, this effect persists during the synthesis process and has a remarkable impact on the late part. The results above expand our cognition of this regulator, and also helpful for comprehensively and systematically reveal its role in flagella system.
2018-10-03 | GSE87852 | GEO
Project description:The circadian clock of the cyanobacterium Synechococcus elongatus PCC 7942 drives oscillations in global mRNA abundances with 24 hour periodicity under constant light conditions. The transcription factor RpaA, a circadian clock-regulated transcription factor, controls the timing of circadian gene expression, but the mechanisms underlying this control are not well understood. Here we show that four RpaA-dependent sigma factors – RpoD2, RpoD6, RpoD5, and SigF2 – are sequentially activated downstream of active RpaA and are required for proper expression of circadian mRNAs. We find that RpoD6, RpoD5, and SigF2 exhibit circadian oscillations with different timing relative to each other at the level of mRNA expression and protein abundance. By measuring global gene expression in strains modified to individually lack rpoD2, rpoD6, rpoD5, and sigF2 we identify how expression of circadian mRNAs – including sigma factor mRNAs – is altered in the absence of each sigma factor. Broadly, our findings suggest that a single transcription factor, RpaA, is sufficient to generate complex circadian expression patterns in part by regulating an interdependent sigma factor cascade.
2019-05-20 | GSE114693 | GEO
Project description:Genetically engineered Salmonella Typhimurium are potent vectors for prophylactic and therapeutic measures against pathogens as well as cancer. This is based on the potent adjuvanticity that supports strong immune responses. The physiology of Salmonella is well understood. It simplifies engineering of both enhanced immune-stimulatory properties as well as safety features, thus, resulting in an appropriate balance between attenuation and efficacy for clinical applications. A major virulence factor of Salmonella is the flagellum. It is also a strong pathogen-associated molecular pattern recognized by extra- and intracellular receptors of immune cells of the host. At the same time, it represents a serious metabolic burden. Accordingly, the bacteria evolved tight regulatory mechanisms that control flagella synthesis in vivo. Here, we systematically investigated the immunogenicity and adjuvant properties of various flagella mutants of Salmonella in vitro and in a mouse cancer model in vivo. We found that mutants lacking the flagellum-specific ATPase FliHIJ or the inner membrane ring FliF displayed the greatest stimulatory capacity and strongest anti-tumor effects, while remaining safe in vivo. Scanning electron microscopy revealed the presence of outer membrane vesicles in the ΔfliF and ΔfliHIJ mutants. Finally, the combination of the ΔfliF and ΔfliHIJ mutations with our previously described attenuated and immunogenic background strain SF102 displayed strong efficacy against the highly resistant cancer cell line RenCa. We thus conclude that manipulating flagella biosynthesis has great potential for the construction of highly efficacious and versatile Salmonella vector strains.
2019-11-25 | GSE116623 | GEO
Project description:An RpaA-dependent sigma factor cascade sets the timing of circadian transcriptional rhythms in Synechococcus elongatus
| PRJNA472248 | ENA
Project description:Flagella-driven motility of Salmonella enterica serovar Typhimurium facilitates host colonization. However, the large extracellular flagellum is also a prime target for the immune system. As consequence, expression of flagella is bistable within a population of Salmonella, resulting in flagellated and non-flagellated subpopulations. This allows the bacteria to maximize fitness in hostile environments. The degenerate EAL-domain protein RflP (formerly YdiV) is responsible for the bistable expression of flagella by directing the flagellar master regulatory complex FlhD4C2 to proteolytic degradation. The environmental cues controlling expression of rflP and thus the bistable flagellar biosynthesis remain ambiguous. Here, we demonstrate that RflP responds to cell envelope stress and alterations of outer membrane integrity. Lipopolysaccharide (LPS) truncation mutants of Salmonella Typhimurium exhibited increasing motility defects due to downregulation of flagellar gene expression. Transposon mutagenesis and genetic profiling revealed that σ24 (RpoE) and Rcs phosphorelay-dependent cell envelope stress response systems sense modifications of lipopolysaccharide, low pH activity of the complement system. This subsequently results in activation of RflP expression and degradation of FlhD4C2 via ClpXP. We speculate that diverse hostile environments inside the host might result in cell envelope damage and would thus trigger the repression of resource-costly and immunogenic flagella biosynthesis via activation of the cell envelope stress response.
2018-04-13 | GSE87447 | GEO
Project description:Upon entering host cells, Salmonella quickly turn off flagella biogenesis to avoid recognition by the host immune system. However, it is not clear which host signal(s) Salmonella senses to initiate flagellum control.During the infection of a host,acid pH acts as an important environmental factor to triggers some genes expression. To investigate the effect of environmental acid signaling on the regulation of Salmonella flagella synthesis, we cultivated Salmonella typhimurium ATCC 14028s to an OD600 of 0.4, and then continued to culture for 2 h at pH 7.0 or pH 5.0. We then performed gene expression profiling analysis using data obtained from RNA-seq of cultured cells at different pH condition.
2022-08-06 | GSE210570 | GEO
Project description:DNA methylation and DNA replication timing were examined across a variety of human tissues and cell lines, applying microarray-based techniques. The analyses revealed that late-replicating DNA was demethylated compared to the methylation of early-replicating regions. DNA methylation: Epstein-Barr-Virus (EBV) transformed B-lymphocyte cell lines GM10849, GM12089, GM12092, GM12093, and GM08714 (ICF) (http://ccr.coriell.org/nigms) were cultured in RPMI-1640 supplemented with 15% FCS (Sigma) at 37oC and 5% CO2. Normal BJ foreskin fibroblasts (NHF cells) at different PDs (36)(34) were cultured in 4:1 DMEM : M-199 supplemented with 15% FCS (Sigma) at 37oC and 5% CO2. Replication timing: EBV-transformed female B-lymphocyte cell lines GM12092 and GM12093 were cultured as above, harvested from logarithmic growth cultures, washed once in ice-cold phosphate-buffered saline, immediately fixed in 70-85-95% ethanol at -20oC, stained with propidium iodide, and sorted into G1 and early-S fractions using a MoFlo cell sorter.
2010-12-01 | E-GEOD-24947 | biostudies-arrayexpress