Emergence of the primordial pre-60S from the 90S pre-ribosome

Ismail, Sherif; Flemming, Dirk; Thoms, Matthias; Gomes-Filho, José Vicente; Randau, Lennart; Beckmann, Roland; Hurt, Ed

doi:10.1016/j.celrep.2022.110640

Cited by 23 publications

(25 citation statements)

References 103 publications

(144 reference statements)

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“…C9orf114 was reported to interact with mRNA (Baltz et al, 2012; Castello et al, 2012) while it was also shown to bind to a specific miRNA and its knockdown causes a reduced level of the mature miRNA, suggesting a role in posttranscriptional regulation (Treiber et al, 2017). The yeast orthologs have been suggested to play a key role in the formation of the large ribosomal subunit (Ismail et al, 2022). Because At5g19300 has not been characterized before, we name this locus ITS1 and refer to one mutant resulting in an amino acid substitution as its1-1 and another one containing a premature stop codon as its1-2 (Figure 2A).…”

Section: Resultsmentioning

confidence: 99%

“…The growth defects observed in knockout alleles of ITS1 indicate the functional importance of ITS1 in other aspects than the response to thermospermine although it is not an essential gene for survival. A recent study has revealed that Upa1 and Upa2, yeast orthologues of SPOUT1/C9orf114, are contained in the primordial pre-60S ribosomal subunit and raised a possibility that they methylate a specific pseudouridine in the pre-60S (Ismail et al, 2022). Multiple mutant alleles of ITS1 will provide a tool for biochemical characterization of ITS1 in future research.…”

Section: Discussionmentioning

confidence: 99%

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RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana

Takahashi

Tanaka

Koyama

et al. 2022

Preprint

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Thermospermine acts in negative regulation of xylem differentiation through enhancing mRNA translation of the members of the SAC51 gene family in Arabidopsis. These mRNAs contain conserved upstream open-reading-frames (uORFs) that are inhibitory to the main ORF translation. To address the mode of action of thermospermine in this process, we have isolated mutants that are insensitive to thermospermine, named its. We show here that four genes responsible for the mutants, its1 to its4, encode a homologue of SPOUT RNA methyl transferase, an rRNA pseudouridine synthase CBF5/NAP57, a putative spliceosome disassembly factor STIPL1/NTR1, and a plant-specific RNA-binding protein PHIP1, respectively. While these mutants except its1 are almost normal in appearance, they enhance the dwarf phenotype of a mutant of ACL5 defective in thermospermine biosynthesis, resulting in tiny-sized plants reminiscent of a double knockout of ACL5 and SACL3, a member of the SAC51 family. We confirmed that the GUS reporter activity from the SAC51 5'-GUS fusion transcript was severely reduced in all of these mutants. These results unveil the importance of RNA processing and modification for the translation of transcripts containing regulatory uORFs.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana

Takahashi

Tanaka

Koyama

et al. 2022

Preprint

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“…The proteins that were however most strongly enriched in Rbp95-TAP were Npa1, Npa2, Dbp6, Dbp7, Dbp9, Rsa3 and Nop8, all belonging to a sub-complex of early pre-60S particles termed the Npa1 complex ( 10 , 42–44 ). A few other proteins involved in early pre-60S maturation (Mak5, Nop4, Nop13) and two mostly uncharacterized proteins (Ygr283c and Ymr310c), which were recently renamed Upa1 and Upa2, and reported to be components of early pre-60S particles ( 45 ), were enriched as well. Together, our results indicate that Rbp95 is bound to 90S and early pre-60S particles, similar to Npa1 complex members and the early pre-60S factors Mak5, Nop4 and Nop13.…”

Section: Resultsmentioning

confidence: 99%

“…Hence, our work may have revealed additional important players, potentially acting in conjunction with Rbp95, in these early pre-60S maturation steps. Indeed, a recent publication revealed Rbp95 to be a stochiometric component of Upa1- or Upa2-purified particles ( 45 ).…”

Section: Discussionmentioning

confidence: 99%

Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation

Bhutada

Favre

Jaafar

et al. 2022

Nucleic Acids Research

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Eukaryotic ribosome synthesis involves more than 200 assembly factors, which promote ribosomal RNA (rRNA) processing, modification and folding, and assembly of ribosomal proteins. The formation and maturation of the earliest pre-60S particles requires structural remodeling by the Npa1 complex, but is otherwise still poorly understood. Here, we introduce Rbp95 (Ycr016w), a constituent of early pre-60S particles, as a novel ribosome assembly factor. We show that Rbp95 is both genetically and physically linked to most Npa1 complex members and to ribosomal protein Rpl3. We demonstrate that Rbp95 is an RNA-binding protein containing two independent RNA-interacting domains. In vivo, Rbp95 associates with helix H95 in the 3′ region of the 25S rRNA, in close proximity to the binding sites of Npa1 and Rpl3. Additionally, Rbp95 interacts with several snoRNAs. The absence of Rbp95 results in alterations in the protein composition of early pre-60S particles. Moreover, combined mutation of Rbp95 and Npa1 complex members leads to a delay in the maturation of early pre-60S particles. We propose that Rbp95 acts together with the Npa1 complex during early pre-60S maturation, potentially by promoting pre-rRNA folding events within pre-60S particles.

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“…3. The genes are ordered according to their function in the assembly of each subunit or ribosome translation function (4, 62, 63).…”

Section: Resultsmentioning

confidence: 99%

Inhibiting ribosome assembly and ribosome translation have distinctly different effects on the abundance and paralogue composition of ribosomal protein mRNAs inSaccharomyces cerevisiae

Shamsuzzaman

Rahman

Bommakanti

et al. 2022

Preprint

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Many mutations in genes for ribosomal proteins and assembly factors cause cell stress and altered cell fate resulting in congenital diseases, collectively called ribosomopathies. Even though all such mutations depress the cell's protein synthesis capacity, they generate many different phenotypes, suggesting that the diseases are not due simply to insufficient protein synthesis capacity. To learn more, we have investigated how the global transcriptome in Saccharomyces cerevisiae responds to reduced protein synthesis generated in two different ways: abolishing the assembly of new ribosomes or inhibiting ribosomal function. Our results show that the mechanism by which protein synthesis is obstructed affects the ribosomal protein transcriptome differentially: ribosomal protein mRNA abundance increases during the abolition of ribosome formation but decreases during the inhibition of ribosome function. Interestingly, the ratio between mRNAs from some, but not all, paralogous genes encoding slightly different versions of a given r-protein change differently during the two types of stress, suggesting that specific ribosomal protein paralogues may contribute to the stress response. Unexpectedly, the abundance of transcripts for ribosome assembly factors and translation factors remains relatively unaffected by the stresses. On the other hand, the state of the translation apparatus does affect cell physiology: mRNA levels for some other proteins not directly related to the translation apparatus also change differentially, though not coordinately with the r-protein genes, in response to the stresses.

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Emergence of the primordial pre-60S from the 90S pre-ribosome

Cited by 23 publications

References 103 publications

RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana

RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana

Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation

Inhibiting ribosome assembly and ribosome translation have distinctly different effects on the abundance and paralogue composition of ribosomal protein mRNAs inSaccharomyces cerevisiae

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