Ontology highlight
ABSTRACT:
PROVIDER: PRJNA616127 | ENA |
REPOSITORIES: ENA
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Project description:The archaeal ribosome is of the eukaryotic type. Genomic and phylogenetic studies have indicated that TACK and Asgard, the closest relatives of eukaryotes, have ribosomes containing eukaryotic ribosomal proteins not found in other archaeal branches, eS25, eS26 and eS30. In our study, we investigated the case of Saccharolobus solfataricus, a crenarchaea belonging to the TACK branch, which mainly uses leaderless mRNAs. We characterized the small ribosomal subunit of S. Solfataricus bound to SD-leadered or leaderless mRNAs. Cryo-EM structures show for the first time archaeal versions of the eS25, eS26 and eS30 proteins bound to the small subunit. In addition, we identify two novel ribosomal proteins named aS33 and aS34 as well as a domain of eS6, that highlight the diversity of archaeal ribosomes. Leaderless mRNAs are bound to the small ribosomal subunit and the 5'-triphosphate group contributes to their binding. Archaeal eS26 is in the mRNA exit channel wrapped around the 3' end of ribosomal RNA as it is in eukaryotes. Its position is not compatible with an SD:antiSD duplex in the mRNA exit channel. Overall, our results suggest a role of eS26 in translation regulation and possible evolutionary routes from archaeal to eukaryotic translation.
2025-05-07 | PXD053103 | Pride
Project description:Genome-wide occupancy of the basal transcription machinery in Saccharolobus solfataricus strain P2 (Sulfolobus solfataricus) after hydrogen peroxide treatment Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.
2020-09-14 | GSE141033 | GEO
Project description:Identification of the proteins from tryptic digests of Saccharolobus solfataricus strain P1 whole-cell proteome followed by nanoLC/OrbitrapFusion MS analysis.
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Project description:Lamins are the main constituents of the nuclear lamina, a fibrillar layer underlyingthe inner nuclear membrane. The nuclear lamina governs chromatinorganization through lamina-associated domainswithin the densely packed heterochromatin regions. Employing cryo-focused ion beam (cryo-FIB) milling in conjunction withcryo-electron tomography (cryo-ET), we mappedthe concentration of nucleosomesat the lamin-chromatin interface. Depletion of lamin A/C induces nanometer-scale chromatin decompaction, macroscopic-scale alterations in gene expression and chromatin-wide alterations of chromatin properties, revealed by 4f-genome-wide analysis. Cryo-electron microscopy (cryo-EM) structural analysis revealed a specific interaction between nucleosomes and the tail domain of lamin A. A unique motif of lamin A that distinguishes it from other lamin isoforms. These findings illuminatethe dynamic interplay between specific lamins and chromatin, shaping chromatin architecture and epigenetic regulation.
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Project description:Saccharolobus solfataricus strain:98/2 U2 Genome sequencing
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Project description:Saccharolobus solfataricus strain:98/2 U1 Genome sequencing
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