Uncultured protist
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA305513 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2993410.fastq.gz | Fastqsanger.gz | |||
| SRR2993411.fastq.gz | Fastqsanger.gz | |||
| SRR2993412.fastq.gz | Fastqsanger.gz | |||
| SRR2993403.fastq.gz | Fastqsanger.gz | |||
| SRR2993404.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 9 |
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Project description:Cleavage and polyadenylation are the final steps of eukaryotic mRNA 3' end formation. The most critical element in humans and other model organisms is the poly(A) signal, an AAUAAA hexamer. We recently discovered that the deeply branching eukaryote – Giardia lamblia uses a different but well-defined poly(A) signal, AGURAA. To better characterize when this evolutionary shift in the poly(A) signal occurred, we performed direct RNA sequencing of four protists within the Metamonada supergroup and two outgroup protists. Both outgroup protists and the non-Giardia Metamonada species use the AAUAAA poly(A) signal, indicating it is the ancestral signal. In contrast, all Giardia species use the WGURAA poly(A) signal, indicating it is a derived feature within Giardia or Fornicata. The change in this ubiquitous regulatory element raises questions about the sequence features that specify genuine poly(A) sites and how to avoid premature cleavage in the coding sequence. Therefore, we used a sequence classifier, a gapped k-mer support vector machine, that could discriminate between WGURAA sites in 3'UTRs and those in the CDS (F1 = 0.97). We found that Giardia lamblia uses nucleotides directly flanking the poly(A) signal for its recognition, with downstream nucleotides being the most important. Another member of the Giardia genus, Giardia muris, uses a different strategy: almost complete depletion of WGURAA hexamers in coding sequences. Ones that remain in the coding sequence can be recognized as poly(A) signals and undergo premature cleavage. These results identify unique features of the Giardia pathogens that could be targeted for drugs and highlight the diversity and evolution of mRNA 3' end formation in eukaryotes.
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Project description:Abstract - 18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. While this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.
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Project description:Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat-stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3’ end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3’ end maturation or metabolism. We quantitatively defined new processing hotspots and identified adenylation as the prevalent non-templated RNA modification at the 3’ ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNAi to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3’ portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late-40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, mRNA translation initiation, and siRNA biogenesis in plants.
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