Herbaspirillum sp. VT-16-41
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA356909 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacillus sp. VT-16-64 Genome sequencing and assembly
| PRJNA351905 | ENA
Project description:Moraxella sp. VT-16-12 Genome sequencing and assembly
| PRJNA391402 | ENA
Project description:Brucellaceae bacterium VT-16-1752 Genome sequencing and assembly
| PRJNA498800 | ENA
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.
2026-05-04 | GSE329534 | GEO
Project description:Azospirillum sp. VT-I1 isolate:VT-I1 Genome sequencing
| PRJNA1144235 | ENA
Project description:Bacillus obstructivus strain:VT-16-70 Genome sequencing and assembly
| PRJNA351908 | ENA
Project description:Fusobacterium sp. 41 strain:41 | isolate:41 Genome sequencing
| PRJNA1426394 | ENA
Project description:Streptococcus sp. VT 162 Genome sequencing
| PRJNA227244 | ENA
Project description:Herbaspirillum sp. Genome sequencing and assembly
| PRJNA1109581 | ENA
Project description:Many tissue-specific stem cells maintain the ability to produce multiple cell types during long periods of non-division, or quiescence. FOXO transcription factors promote quiescence and stem cell maintenance, but the mechanisms by which FOXO proteins promote multipotency during quiescence are still emerging. The single FOXO ortholog in C. elegans, daf-16, promotes entry into a quiescent and stress-resistant larval stage called dauer in response to adverse environmental cues. During dauer, stem and progenitor cells maintain or re-establish multipotency to allow normal development to resume after dauer. We find that during dauer, daf-16/FOXO prevents epidermal stem cells (seam cells) from prematurely adopting differentiated, adult characteristics. In particular, dauer larvae that lack daf-16 misexpress collagens that are normally adult-enriched. Using col-19p::gfp as an adult cell fate marker, we find that all major daf-16 isoforms contribute to opposing col-19p::gfp expression during dauer. By contrast, daf-16(0) larvae that undergo non-dauer development do not misexpress col-19p::gfp. Adult cell fate and the timing of col-19p::gfp expression are regulated by the heterochronic gene network, including lin-41 and lin-29. lin-41 encodes an RNA-binding protein orthologous to LIN41/TRIM71 in mammals, and lin-29 encodes a conserved zinc finger transcription factor. In non-dauer development lin-41 opposes adult cell fate by inhibiting the translation of lin-29, which directly activates col-19 transcription and promotes adult cell fate. We find that during dauer, lin-41 blocks col-19p::gfp expression, but surprisingly, lin-29 is not required in this context. Additionally, daf-16 promotes the expression of lin-41 in dauer larvae. The col-19p::gfp misexpression phenotype observed in dauer larvae with reduced daf-16 requires the downregulation of lin-41, but does not require lin-29. Taken together, this work demonstrates a novel role for daf-16/FOXO as a heterochronic gene that promotes expression of lin-41/TRIM71 to contribute to multipotent cell fate in a quiescent stem cell model.
2021-10-09 | GSE179166 | GEO