Maturation of small nucleolar RNAs: from production to function

Webster, Sarah F.; Ghalei, Homa

doi:10.1080/15476286.2023.2254540

Cited by 6 publications

(1 citation statement)

References 298 publications

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“…The expression of snoRNAs and their host genes has been reported to involve multistep regulation, including transcription from dual-initiation promoters [78], Nonsense-Mediated Decay [79] and alternative snoRNA processing [80], with snoRNA stability and terminal stem formation also contributing to snoRNA expression expression levels [81]. In humans, intronic snoRNAs typically mature through splicing, debranching and exonucleolytic processing, or through an alternative pathway involving endonucleolytic cleavage [82]. Drosophila snoRNA processing is poorly described but is possible that dephosphorylation of Cdk11 is required for regulation of one or more analogous steps in this maturation pathway.…”

Section: Regulatory Roles Of Cdk11 Dephosphorylationmentioning

confidence: 99%

Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function

Campbell,

Aljabri,

Hesketh

et al. 2024

Preprint

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Organisation of the transcription cycle is facilitated by the reversible phosphorylation of the C-terminal domain of RNA Polymerase II (RNAPII-CTD) and its accessory factors. The PNUTS-PP1 protein phosphatase is crucial for mRNA synthesis and processing, yet the complete spectrum of its physiological targets in these processes remain elusive. Here, using quantitative phosphoproteomics, we discover that Cdk11, in addition to various spliceosomal and RNA processing factors, associates with PNUTS, and that disruption of PP1-binding results in hyperphosphorylation of Cdk11 at an evolutionarily conserved Serine residue, seven amino acid residues C-terminal to DFG residues in the activation loop. In vitro experiments reveal a role for Ser DFG+7 in modulating Cdk11 kinase activity towards RNAPII-CTD Ser5. Making use of a novel technique to conditionally disrupt PP1 binding, we show that PNUTS-PP1 normally serves to restrain Cdk11 phosphorylation in vivo. Mutational analysis shows that cdk11 is not only essential for survival but also plays a widespread role in regulating normal mRNA expression and splicing. Notably, we find that a phosphomimetic mutation in cdk11 exhibits distinct biological effects compared to loss of cdk11 function, including defective processing of intronic small nucleolar RNAs, diminished intronic RNA Pol II velocity, and a decrease in intergenic transcription. These findings underscore physiologically significant roles of Cdk11 dephosphorylation by PNUTS-PP1 in the regulation of mRNA transcription and processing.

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Section: Regulatory Roles Of Cdk11 Dephosphorylationmentioning

confidence: 99%

Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function

Campbell,

Aljabri,

Hesketh

et al. 2024

Preprint

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Plant ribosomes as a score to fathom the melody of 2’- O -methylation across evolution

Neumann,

Gaspin,

Sáez-Vásquez

2024

RNA Biology

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2’- O -ribose methylation (2’- O -Me) is one of the most common RNA modifications detected in ribosomal RNAs (rRNA) from bacteria to eukaryotic cells. 2’- O -Me favours a specific RNA conformation and protects RNA from hydrolysis. Moreover, rRNA 2’- O -Me might stabilize its interactions with messenger RNA (mRNA), transfer RNA (tRNA) or proteins. The extent of rRNA 2’- O -Me fluctuates between species from 3–4 sites in bacteria to tens of sites in archaea, yeast, algae, plants and human. Depending on the organism as well as the rRNA targeting site and position, the 2’- O -Me reaction can be carried out by several site-specific RNA methyltransferases (RMTase) or by a single RMTase associated to specific RNA guides. Here, we review current progresses in rRNA 2’- O -Me (sites/Nm and RMTases) in plants and compare the results with molecular clues from unicellular (bacteria, archaea, algae and yeast) as well as multicellular (human and plants) organisms.

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Differential roles of putative arginine fingers of AAA⁺ATPases Rvb1 and Rvb2

Warnock,

Ball,

Najmi

et al. 2024

Preprint

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The evolutionarily conserved AAA+ ATPases Rvb1 and Rvb2 proteins form a heteromeric complex (Rvb1/2) required for assembly or remodeling of macromolecular complexes in essential cellular processes ranging from chromatin remodeling to ribosome biogenesis. Rvb1 and Rvb2 have a high degree of sequence and structural similarity, and both contain the classical features of ATPases of their clade, including an N-terminal AAA+ subdomain with the Walker A motif, an insertion domain that typically interacts with various binding partners, and a C-terminal AAA+ subdomain containing a Walker B motif, the Sensor I and II motifs, and an arginine finger. In this study, we find that despite the high degree of structural similarity, Rvb1 and Rvb2 have distinct active sites that impact their activities and regulation within the Rvb1/2 complex. Using a combination of biochemical and genetic approaches, we show that replacing the homologous arginine fingers of Rvb1 and Rvb2 with different amino acids not only has distinct effects on the catalytic activity of the complex, but also impacts cell growth, and the Rvb1/2 interactions with binding partners. Using molecular dynamics simulations, we find that changes near the active site of Rvb1 and Rvb2 cause long-range effects on the protein dynamics in the insertion domain, suggesting a molecular basis for how enzymatic activity within the catalytic site of ATP hydrolysis can be relayed to other domains of the Rvb1/2 complex to modulate its function. Further, we show the impact that the arginine finger variants have on snoRNP biogenesis and validate the findings from molecular dynamics simulations using a targeted genetic screen. Together, our results reveal new aspects of the regulation of the Rvb1/2 complex by identifying a relay of long-range molecular communication from the ATPase active site of the complex to the binding site of cofactors. Most importantly, our findings suggest that despite high similarity and cooperation within the same protein complex, the two proteins have evolved with unique properties critical for the regulation and function of the Rvb1/2 complex.

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Maturation of small nucleolar RNAs: from production to function

Cited by 6 publications

References 298 publications

Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function

Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function

Plant ribosomes as a score to fathom the melody of 2’- O -methylation across evolution

Differential roles of putative arginine fingers of AAA⁺ATPases Rvb1 and Rvb2

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Maturation of small nucleolar RNAs: from production to function

Cited by 6 publications

References 298 publications

Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function

Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function

Plant ribosomes as a score to fathom the melody of 2’- O -methylation across evolution

Differential roles of putative arginine fingers of AAA+ATPases Rvb1 and Rvb2

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Product

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Differential roles of putative arginine fingers of AAA⁺ATPases Rvb1 and Rvb2