Ontology highlight
ABSTRACT:
PROVIDER: PRJNA834898 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19086128.fastq.gz | Fastqsanger.gz |
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Project description:Yeast large ribosomal subunit (LSU) precursors are subject to substantial changes in protein composition during their maturation due to coordinated transient interactions with a large number of ribosome biogenesis factors and due to the assembly of ribosomal proteins. These compositional changes go along with stepwise processing of LSU rRNA precursors and with specific rRNA folding events, as revealed by recent cryo-electron microscopy analyses of late nuclear and cytoplasmic LSU precursors. Here we aimed to analyze changes in the spatial rRNA surrounding of selected ribosomal proteins during yeast LSU maturation. For this we combined a recently developed tethered tertiary structure probing approach with both targeted and high-throughput readout strategies. Several structural features of late LSU precursors were faithfully detected by this procedure. In addition, the obtained data let us suggest that early rRNA precursor processing events are accompanied by a global transition from a flexible to a spatially restricted rRNA conformation. For intermediate LSU precursors, a number of structural hallmarks could be addressed which include the fold of the internal transcribed spacer between 5.8S rRNA and 25S rRNA, the orientation of the central protuberance and the spatial organization of the interface between LSU rRNA domains I and III.
2017-04-01 | GSE97276 | GEO
Project description:Because plants are immobile, they have developed intricate mechanisms to sense and absorb nutrients, adjusting their growth and development accordingly. Sulfur is an essential macroelement, but our understanding of its metabolism and homeostasis is limited. LSU (RESPONSE TO LOW SULFUR) proteins are plant-specific proteins with unknown molecular functions and were first identified during transcriptomic studies on sulfur deficiency in Arabidopsis. These proteins are crucial hubs that integrate environmental signals and are involved in the response to various stressors. Herein, we report the direct involvement of LSU proteins in primary sulfur metabolism for the first time. Our findings revealed that the quadruple lsu mutant, q-lsu-KO, which was grown under nonlimiting sulfate conditions, exhibited a molecular response resembling that of sulfur-deficient wild-type plants. This led us to explore the interactions of LSU proteins with sulfate reduction pathway enzymes. We found that all LSU proteins interact with ATPS1 and ATPS3 isoforms of ATP sulfurylase, all three isoforms of adenosine 5´phosphosulfate reductase (APR), and sulfite reductase (SiR). Additionally, in vitro assays revealed that LSU1 enhances the enzymatic activity of SiR. These results highlight the supportive role of LSU proteins in the sulfate reduction pathway.
2024-12-11 | GSE271678 | GEO
Project description:Ribosome assembly, which requires the temporal and spatial coordination of multiple interconnected processes, is essential for life in every known organism. The large ribosomal subunit (LSU) of Escherichia coli (E. coli) contains two RNA molecules, 23S and 5S, which serve as a platform for assembly. Ribosomal RNA (rRNA) modifications and processing are key steps in this process. We simultaneously detect and quantify eight classes of 23S rRNA modifications in the mature 50S LSU from E. coli cells expressing wild-type DbpA, the 50S LSU from cells expressing the helicase-inactive R331A DbpA construct, and two LSU intermediates, 35S and 45S, which accumulate in distinct ribosome maturation pathways in R331A DbpA-expressing cells. Additionally, we analyze the 3′-end processing of 23S and 5S rRNA in all these particles. Most 23S rRNA modifications are incorporated into the 35S and 45S intermediates at levels comparable to those in the 50S LSU from both wild-type and R331A DbpA-expressing cells, indicating that modification enzymes complete their functions before 35S and 45S accumulation. However, three enzymes exhibit differential modification patterns. RlmN incorporates N²-methyladenosine (m²A) at position 2507 more extensively in the 50S LSU from wild-type DbpA-expressing cells than in the 35S, 45S, and 50S LSU from R331A DbpA-expressing cells. Conversely, RluC incorporates pseudouridine (Ψ) at position 2508 at lower levels in the 50S LSU from wild-type DbpA-expressing cells than in the 35S, 45S, and 50S LSU from R331A DbpA-expressing cells. The RluF enzyme incorporates Ψ at position 2508 at a lower level in the 50S LSU from R331A DbpA-expressing cells than in the 35S and 45S intermediates and the 50S LSU from wild-type DbpA-expressing cells. Since the pathways leading to 35S and 45S account for only ~50% of total ribosome assembly in R331A DbpA-expressing cells, these findings reveal that RluF activity is reduced in a subset of maturation pathways. The 3′ end of 23S rRNA is less mature in the early-stage LSU intermediate, 35S, and more mature in the late-stage LSU intermediate, 45S. Interestingly, the 3′ end of 5S rRNA is less processed in the 45S than in the 35S, suggesting that 5S rRNA in the 45S intermediate matures during the final steps of large subunit ribosome assembly. A complete understanding of ribosome assembly demands a precise characterization of ribosome assembly pathways and processes across diverse cellular conditions. This study reveals critical insights into rRNA modifications and processing dynamics in bacterial ribosomes under stress.
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