Limits...
Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution.

Hector RD, Burlacu E, Aitken S, Le Bihan T, Tuijtel M, Zaplatina A, Cook AG, Granneman S - Nucleic Acids Res. (2014)

Bottom Line: However, detailed insights into the function of assembly factors and ribosomal RNA folding events are lacking.We show that RNA restructuring events coincide with the release of assembly factors and predict that completion of the head domain is required before the Rio1 kinase enters the assembly pathway.Collectively, our results suggest that 40S assembly factors regulate the timely incorporation of ribosomal proteins by delaying specific folding steps in the 3' major domain of the 20S pre-ribosomal RNA.

View Article: PubMed Central - PubMed

Affiliation: Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3JD, UK.

Show MeSH

Related in: MedlinePlus

40S subunit maturation in Saccharomyces cerevisiae. (A) Schematic representation of the cytoplasmic 40S synthesis pathway. (B and C) Pre-40S particles at different stages of assembly are purified using strains expressing TAP-or HTP-tagged assembly factors. Particles are chemically modified (B), RNA is extracted and gel purified 20S and 18S rRNAs are analyzed on a Bioanalyzer (C). (D and E) cDNA libraries, generated by random priming, were PCR amplified and (E) sequenced on a HiSeq. (F) Chemically modified samples were compared to solvent treated samples using a two-channel Poisson expectation maximization algorithm (TCMPEM) to identify nucleotides that had the highest likelihood of being modified.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4231735&req=5

Figure 1: 40S subunit maturation in Saccharomyces cerevisiae. (A) Schematic representation of the cytoplasmic 40S synthesis pathway. (B and C) Pre-40S particles at different stages of assembly are purified using strains expressing TAP-or HTP-tagged assembly factors. Particles are chemically modified (B), RNA is extracted and gel purified 20S and 18S rRNAs are analyzed on a Bioanalyzer (C). (D and E) cDNA libraries, generated by random priming, were PCR amplified and (E) sequenced on a HiSeq. (F) Chemically modified samples were compared to solvent treated samples using a two-channel Poisson expectation maximization algorithm (TCMPEM) to identify nucleotides that had the highest likelihood of being modified.

Mentions: Figure 1A shows a schematic representation of our current knowledge about the cytoplasmic steps of yeast 40S maturation. As in bacteria, small subunit assembly in yeast involves many restructuring and/or remodeling steps; however, these events are still poorly understood. The earliest pre-40S complexes contain an almost complete set of r-proteins, a handful of assembly factors and the endonuclease Nob1 that performs the final cleavage event at site D (Figure 1A). The majority of assembly factors associate with pre-40S complexes in the nucleus and, upon entry into the cytoplasm, are believed to progressively dissociate from intermediates. However, it is not entirely clear in which order these factors are released (Figure 1A). CRAC UV cross-linking and cryo-electron microscopy (cryo-EM) experiments have localized binding sites for many assembly factors (5,6). Several assembly factors cross-linked near r-protein binding sites and it was proposed that this could interfere with stable binding of r-proteins to pre-40S (5). Their presence is also incompatible with binding of mRNA, tRNAs and translation initiation factors, indicating that they block premature translation initiation (5,6).


Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution.

Hector RD, Burlacu E, Aitken S, Le Bihan T, Tuijtel M, Zaplatina A, Cook AG, Granneman S - Nucleic Acids Res. (2014)

40S subunit maturation in Saccharomyces cerevisiae. (A) Schematic representation of the cytoplasmic 40S synthesis pathway. (B and C) Pre-40S particles at different stages of assembly are purified using strains expressing TAP-or HTP-tagged assembly factors. Particles are chemically modified (B), RNA is extracted and gel purified 20S and 18S rRNAs are analyzed on a Bioanalyzer (C). (D and E) cDNA libraries, generated by random priming, were PCR amplified and (E) sequenced on a HiSeq. (F) Chemically modified samples were compared to solvent treated samples using a two-channel Poisson expectation maximization algorithm (TCMPEM) to identify nucleotides that had the highest likelihood of being modified.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231735&req=5

Figure 1: 40S subunit maturation in Saccharomyces cerevisiae. (A) Schematic representation of the cytoplasmic 40S synthesis pathway. (B and C) Pre-40S particles at different stages of assembly are purified using strains expressing TAP-or HTP-tagged assembly factors. Particles are chemically modified (B), RNA is extracted and gel purified 20S and 18S rRNAs are analyzed on a Bioanalyzer (C). (D and E) cDNA libraries, generated by random priming, were PCR amplified and (E) sequenced on a HiSeq. (F) Chemically modified samples were compared to solvent treated samples using a two-channel Poisson expectation maximization algorithm (TCMPEM) to identify nucleotides that had the highest likelihood of being modified.
Mentions: Figure 1A shows a schematic representation of our current knowledge about the cytoplasmic steps of yeast 40S maturation. As in bacteria, small subunit assembly in yeast involves many restructuring and/or remodeling steps; however, these events are still poorly understood. The earliest pre-40S complexes contain an almost complete set of r-proteins, a handful of assembly factors and the endonuclease Nob1 that performs the final cleavage event at site D (Figure 1A). The majority of assembly factors associate with pre-40S complexes in the nucleus and, upon entry into the cytoplasm, are believed to progressively dissociate from intermediates. However, it is not entirely clear in which order these factors are released (Figure 1A). CRAC UV cross-linking and cryo-electron microscopy (cryo-EM) experiments have localized binding sites for many assembly factors (5,6). Several assembly factors cross-linked near r-protein binding sites and it was proposed that this could interfere with stable binding of r-proteins to pre-40S (5). Their presence is also incompatible with binding of mRNA, tRNAs and translation initiation factors, indicating that they block premature translation initiation (5,6).

Bottom Line: However, detailed insights into the function of assembly factors and ribosomal RNA folding events are lacking.We show that RNA restructuring events coincide with the release of assembly factors and predict that completion of the head domain is required before the Rio1 kinase enters the assembly pathway.Collectively, our results suggest that 40S assembly factors regulate the timely incorporation of ribosomal proteins by delaying specific folding steps in the 3' major domain of the 20S pre-ribosomal RNA.

View Article: PubMed Central - PubMed

Affiliation: Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3JD, UK.

Show MeSH
Related in: MedlinePlus