Ontology highlight
ABSTRACT:
PROVIDER: PRJNA977579 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24760948.fastq.gz | Fastqsanger.gz |
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Project description:This study provides comparative RNA-seq datasets for four freshwater bacterial isolates, Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738, cultured under iron-replete (+100 uM FeCl3) and iron-limited (no FeCl3) conditions. Iron availability is a key factor influencing bacterial fitness, and iron limitation is known to activate siderophore biosynthesis, iron transport, and homeostasis pathways. A total of eight libraries generated in 2024 and 2025 were analyzed, comprising 349.9 million processed reads. Reference-guided mapping rates varied among strains, with higher mapping efficiency observed in Pseudomonas, Herbaspirillum, and Pantoea, while Micrococcus showed comparatively lower mapping rates under both conditions. Differential expression analysis revealed strain-specific responses to iron limitation. Genes related to pyoverdine and ferrichrome uptake were enriched in Pseudomonas and Herbaspirillum, enterobactin-associated pathways were prominent in Pantoea, and genes associated with siderophore production, heme utilization, and Fe-S cluster assembly were identified in Micrococcus. Raw sequencing data are available in the NCBI Sequence Read Archive under BioProject PRJNA1456794, and processed data are deposited in a public repository. These datasets provide a valuable resource for understanding bacterial adaptation to iron availability and for comparative transcriptomic analyses.
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Project description:Bacterial regulatory RNAs (sRNAs) are commonly short non-coding RNAs that function as pleiotropic regulators by post-transcriptionally impacting mRNA stability and/or translation. They play significant roles in bacterial physiology and are typically expressed in response to specific environmental stimuli such as nutrient limitation. The bacterial pathogen Staphylococcus aureus faces decreased access to essential metal ions, including iron, in the mammalian host in a process called nutritional immunity. In response to host-mediated iron limitation, S. aureus expresses the sRNA IsrR, which coordinates an iron-sparing response by downregulating the expression of mRNAs coding for iron-requiring proteins. Herein, we utilized MS2-Affinity Purification coupled with RNA Sequencing (MAPS) to reveal the in vivo IsrR interaction network. Analysis of co-purified RNAs revealed previously unpredicted putative IsrR targets coding for proteins associated with iron-requiring processes. We validated that IsrR directly interacts with eight of these targets in vitro. We demonstrate physiological roles for IsrR in mediating heme biosynthesis, aerobic respiration, and the metabolism of oxygen radicals. These activities are critical for pathogenesis, and this study establishes how S. aureus leverages these processes to adapt to iron scarcity, which is commonly encountered in the mammalian host.
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