Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The small RNA ArcZ coordinates contact-dependent antibacterial killing and diffusible antifungal inhibition via the transcription factor SlyA in Dickeya solani

ABSTRACT: Bacterial phytopathogens deploy diverse antimicrobial systems, including diffusible secondary metabolites and contact-dependent secretion apparatuses, to compete with coinhabiting microorganisms during host colonization. How the production of these distinct weapons is coordinated remains incompletely understood. Here, we identify a two-tier regulatory cascade through which the Hfq-dependent small RNA (sRNA) ArcZ controls both antibacterial and antifungal antagonism in the phytopathogen Dickeya solani. High-throughput RNA interactome analysis (RIL-seq) shows that ArcZ interacts broadly across the transcriptome and directly base-pairs with the 5′ untranslated region of the mRNA encoding the MarR-family transcription factor SlyA, activating its translation. SlyA subsequently binds directly to selected promoter regions within the solanimycin biosynthetic cluster (sol) and the type VI secretion system (T6SS) loci and activates their transcription. The ArcZ-SlyA axis is required for solanimycin‑mediated antifungal activity against Kluyveromyces lactis and for T6SS-dependent killing of the sympatric pathogen Pectobacterium atrosepticum, demonstrating that the D. solani T6SS mediates interbacterial competition. A compensatory base-pairing mutation between ArcZ and slyA restores both competitive phenotypes, establishing this post-transcriptional interaction as a direct upstream determinant. These findings establish a regulatory architecture in which an sRNA activates a transcriptional regulator to coordinate diffusible antifungal and contact-dependent antibacterial activities.

ORGANISM(S): Dickeya solani

PROVIDER: GSE347875 | GEO | 2026/09/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Host infection selects for sRNA variants that drive bacterial social cheating

Project description:Single-nucleotide mutations in regulatory small RNAs (sRNAs) represent a largely unexplored route to social cheating during bacterial infection. Here we show that arcZ, encoding a conserved Hfq-dependent sRNA in the plant pathogen Dickeya solani, undergoes recurrent single-nucleotide mutations during potato tuber infection. Five distinct arcZ alleles define a graded series of ArcZ functional impairment in which antifungal and protease activities are progressively reduced while virulence is compromised only in a subset of alleles. All five variants gain a fitness advantage exclusively during co-infection with wild-type arcZ1 cells, an advantage that is strongest when variants are rare, declines as cheater frequency increases, and correlates with declining total bacterial productivity, the canonical signature of social cheating and a tragedy of the commons.[kp1.1] No fitness benefit is detected in vitro. Transcriptomic profiling of five arcZ variants identifies a conserved core of 132 downregulated genes enriched in secreted and diffusible functions. Systematic genetic dissection, supported by quantitative proteomics, establishes BudAB-dependent acetoin production as the dominant cooperative public good exploited during co-infection. Wild-type arcZ1 cells divert pyruvate flux toward acetoin via the BudAB pathway, maintaining a less acidic tissue environment that sustains disease progression; arcZ variants, which repress this pathway, exploit the resulting pH buffering without contributing to it. These results establish pleiotropic regulatory sRNAs as a previously unrecognized class of mutational targets for the emergence of social cheaters during host infection.

2026-06-13 | GSE334754 | GEO

RNA-seq data of Escheirchia coli K12 MG1655 of overexpression of GcvB, MicA, ArcZ, RyhB or CyaR sRNAs

Project description:To study the regulatory outcome of Hfq-mediated sRNA-target interactions, we measured the change in gene expression following overexpression of each of five well-established sRNAs: GcvB, MicA, ArcZ, RyhB and CyaR. For each of the studied sRNAs we applied RNA-seq to two E. coli K-12 MG1655 strains: (1) a WT strain or a strain deleted of the sRNA gene; (2) a strain overexpressing the sRNA, either artificially from a plasmid or from the endogenous sRNA gene by changing the growth condition. For GcvB induction, the E. coli K-12 MG1655 Z1 gcvB::Cm, pZA12-gcvB and the E. coli K-12 MG1655 Z1 gcvB::Cm, pTP-011 strains were used. For MicA overexpression the E. coli K-12 MG1655lacIq pBRplac, pEF21-Hfq and the E. coli K-12 MG1655lacIq pMicA, pEF21-Hfq strains were used. For ArcZ induction the E. coli K-12 MG1655 Z1 arcZ::Cm, pZE12-ArcZ and the E. coli K-12 MG1655 Z1 arcZ::Cm, pJV300 strains were used. For RyhB overexpression the E. coli K-12 MG1655 ryhB::Cm and the E. coli K-12 MG1655 were used. For CyaR induction the E. coli K-12 MG1655 Z1 cyaR::Cm, pZE12-CyaR and the E. coli K-12 MG1655 Z1 cyaR::Cm, pJV300 strains were used. All E. coli strains used in this study were grown overnight in Luria Bertani (LB) medium at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB medium, and re-grown with shaking at 37 °C to exponential phase, for GcvB (OD600 = 0.3) and for RyhB (OD600 = 0.5), or to stationary phase, for ArcZ WT, ArcZ M1, ArcZ M2 and CyaR (OD600 = 1.0) and for MicA (grown for 6 hr). For induction of ArcZ and GcvB, IPTG was added (1mM, 20 min). MicA was constitutively expressed and further induced at the end of growth with IPTG (1mM, 20 min). For induction of RyhB, the iron chelator 2,2'-Dipyridyl was added (200 μM, 30 min).

2020-03-03 | E-MTAB-8229 | biostudies-arrayexpress

Project description:Erwinia amylovora sRNA ArcZ RNAseq

| PRJNA543432 | ENA

RNA interactome profiling in hypervirulent Klebsiella pneumoniae reveals small RNA ArcZ as an inhibitor of mucoviscosity and virulence

Project description:Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging human pathogen causing invasive infection in immune-competent hosts. The hypervirulence is strongly linked to the overproduction of hypermucovisous capsule, but the underlining regulatory mechanism of hypermucoviscosity (HMV) has been elusive, especially at the post-transcriptional level mediated by small RNAs (sRNAs). Using a recently developed RNA interactome profiling approach, we have investigated the Hfq-associated sRNA regulatory network and established the first in vivo RNA-RNA interactome in HvKP. Our data reveal numerous interactions between sRNAs and HMV-related mRNAs, and identify a plethora of sRNA that inhibit or promote HMV. One of the strongest repressors of HMV was ArcZ, a conserved sRNA in the Enterobacteriaceae family. We found that ArcZ is activated by the master regulator of catabolite repression Crp, and down-regulates the expression of mlaA encoding an outer-membrane lipoprotein, leading to decreased HMV and virulence attenuation in mice. ArcZ significantly reduced HMV in several carbapenem-resistant and hypervirulent clinical isolates with diverse genetic background, suggesting it is an antisense RNA inhibitor of HMV with therapeutic potential. In summary, our work provides a comprehensive map of the RNA-RNA interaction network of HvKP and identifies ArcZ as a conserved repressor of HMV, providing novel insights into the mechanisms of posttranscriptional regulations of virulence.

2024-07-17 | GSE260738 | GEO

RNA-seq data to map the AtsR regulon in B. cenocepacia

Project description:In this study, we embark on a journey to unravel the profound impact of atsR (Adherence and T6SS Regulator) gene deletion on the transcriptome and the proteome of B. cenocepacia K56-2 upon growth in synthetic CF medium (SCFM), the most in-vivo-like culturing medium. Our insights, derived from RNA-seq analysis and label-free LC-MS-based proteomics, validated by multiple reaction monitoring (MRM) analysis, reveal that AtsR's influence extends beyond adhesion, T6SS and the two above QSs, encompassing valdiazen QS, phenylacetic acid signaling system, diffusible signaling factor production, and other pathogenesis-modulating elements such as alternative sigma factors, small regulatory RNAs, and several chaperones.

2026-03-31 | E-MTAB-13688 | biostudies-arrayexpress

A widely-occurring family of pore-forming effectors broadens the impact of the Serratia Type VI secretion system

Project description:The ability to compete with diverse competitors is essential for bacteria to succeed in microbial communities. A widespread strategy for inter-bacterial competition is the delivery of antibacterial toxins, or effector proteins, directly into rival cells using the Type VI secretion system (T6SS). Whilst a large number of broad-spectrum enzymatic T6SS effectors have been described, relatively few which form pores in target cell membranes have been reported. Here, we describe a widely-occurring new family of T6SS-dependent pore-forming effectors, exemplified by Ssp4 of Serratia marcescens Db10. We show that Ssp4 forms cation-selective pores in vitro and use molecular dynamics simulations to support a high resolution structural model of a tetrameric membrane pore formed by Ssp4. Notably, the ion selectivity of Ssp4, its distribution and its impact on intoxicated cells is distinct from that of Ssp6, the other cation-selective pore-forming toxin delivered by the same T6SS. We further discovered that Ssp4 is active against a wider range of target species than Ssp6, highlighting that T6SS effectors are not always broad-spectrum. Finally, use of Tn-seq to identify Ssp4-resistant mutants revealed that a mucA mutant of Pseudomonas fluorescens, which overproduces extracellular polysaccharide, provides resistance to T6SS attacks. We conclude that possession of two distinct T6SS-dependent pore-forming toxins may be a common strategy to ensure effective de-energisation of closely- and distantly-related competitors.

2025-10-31 | GSE301252 | GEO

New insights into antifungal resistance mechanisms in Fusarium species revealed by high throughput sequencing

Project description:Fusarium spp. are fungal pathogens of humans and plants. Fusarium oxysporum and Fusarium solani are important species isolated from infections such as onychomycosis, fungal keratitis, invasive infections, and disseminated diseases. These pathologies have a very difficult therapeutic management and poor therapeutic responses, especially in patients with disseminated infection. Little information is available regarding the molecular mechanisms responsible for antifungal resistance in these fungi. methods: In this study, we performed a quantitative analysis of the transcriptional profile of F. oxysporum and F. solani, challenged with amphotericin B (AMB) and posaconazole (PSC) using RNA-seq. Quantitative real-time reverse transcription PCR (qRT-PCR) was used to validate the results results: Several genes related to mechanisms of antifungal resistance such as efflux pumps, ergosterol pathway synthesis, and responses to oxidative stress were found. Genes such as ERG11, ERG5, the Major Facilitator Superfamily (MFS), thioredoxin, and different dehydrogenase genes may explain the reduced susceptibility of Fusarium spp. against azoles and the possible mechanisms that may play an important role in induced resistance against polyenes. conclusions: Important differences in the levels of transcriptional expression were found between F. oxysporum and F. solani exposed to the two different antifungal treatments. Knowledge on the gene expression profiles and gene regulatory networks in Fusarium spp. during exposure to antifungal compounds, may help to identify possible molecular targets for the development of novel, better, and more specific therapeutic compounds. profile transcriptional of Fusarium spp changed to antifungal treatments in vitro

2016-06-01 | E-GEOD-82060 | biostudies-arrayexpress

Small RNA directs symbiosis, virulence, and natural products biosynthesis in entomopathogenic bacteria

Project description:Rapid modulation of gene expression is a key feature for the success of bacteria, particularly for those that rapidly have to adapt to different niches. The lifecycles of Photorhabdus and Xenorhabdus involve a mutualistic association with nematodes as well as an entomopathogenic phase1,2, both of which rely on the production of numerous specialized metabolites (SMs) 3,4. Several regulators have been previously implicated in the regulation of SM production in these genera3,4. However, the molecular underpinnings regulating SM production and the role of small regulatory RNAs (sRNAs) in this process are unknown. Here we describe the mechanism underlying RNA-mediated control of SM synthesis. We show that the Hfq-dependent sRNA, ArcZ, is an essential requirement for SM production. We discovered that ArcZ directly base-pairs with the mRNA encoding HexA, a key repressor of SM genes. We further demonstrate that the ArcZ regulon is not restricted to SM production, but rather modulates up to ~15% of the transcriptional output in both Photorhabdus and Xenorhabdus. Together, our study shows that sRNAs are crucial for SM production in these species, reveals previously unknown targets for biosynthetic pathway manipulations, and offers a new tool for the (over)production, isolation and identification of unknown natural products.

2020-08-25 | PXD019095 | Pride

Specific and pleiotropic patterns of mRNA regulation by ArcZ

Project description:The small RNA, ArcZ (previously RyhA/SraH), was discovered in several genome-wide screens in Escherichia coli and Salmonella. Its high degree of genomic conservation, its frequent recovery by shotgun sequencing, and its association with the RNA chaperone, Hfq, identified ArcZ as an abundant enterobacterial “core” small RNA of unknown function. Here, we report that ArcZ acts as a post-transcriptional regulator in Salmonella, repressing the mRNAs of the widely distributed sdaCB (serine uptake) and tpx (oxidative stress) genes, and of STM3216, a horizontally acquired methyl-accepting chemotaxis protein (MCP). Both sdaCB and STM3216 are regulated by sequestration of the ribosome binding site. In contrast, the tpx mRNA is targeted in the coding sequence (CDS), arguing that CDS targeting is more common than appreciated. Transcriptomic analysis of an arcZ deletion strain further argued for the existence of a distinct set of Salmonella loci specifically regulated by ArcZ. In contrast, increased expression of the sRNA altered the steady-state levels of >16% (≥750) of all Salmonella mRNAs, and rendered the bacteria non-motile. Deep sequencing detected a dramatically changed profile of Hfq-bound sRNAs and mRNAs suggesting that the unprecedented degree of pleiotropic regulation might in part be caused by titration of Hfq binding by ArcZ.

2009-10-19 | GSE17771 | GEO

New insights into antifungal resistance mechanisms in Fusarium species revealed by high throughput sequencing

2016-06-01 | GSE82060 | GEO