Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes

Panasenko, Olesya O.; Somasekharan, Syam Prakash; Villányi, Zoltán; Zagatti, Marina; Bezrukov, Fedor; Rashpa, Ravish; Cornut, Julien; Iqbal, Jawad; Longis, Marion; Carl, Sarah H.; Peña, Cohue; Panse, Vikram Govind; Collart, Martine A.

doi:10.1038/s41594-018-0179-5

Cited by 109 publications

(185 citation statements)

References 59 publications

(74 reference statements)

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“…Since the functionality of Ccr4-Not extends far beyond mRNA degradation, binding to late initiation complexes could also be involved in entirely different processes such as co-translational assembly of multi-subunit complexes as recently suggested for SAGA complex and proteasome (28,29). The diverse activities of the truly multifunctional Ccr4-Not complex and its relationship to the translation machinery will be further dissected in future studies.…”

Section: Discussionmentioning

confidence: 88%

The Ccr4-Not complex monitors the translating ribosome for codon optimality

Buschauer

Matsuo

Chen

et al. 2019

Preprint

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Control of mRNA decay rate is intimately connected to translation elongation but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. Using a combination of cryo-electron microscopy, ribosome profiling and mRNA stability assays we show recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site. This interaction only occurs when the ribosome lacks accommodated A-site tRNA, indicative of low codon optimality. Loss of Not5 results in the inability of the mRNA degradation machinery to sense codon optimality. Our analysis elucidates a physical link between the Ccr4-Not complex and the ribosome providing mechanistic insight into the coupling of decoding efficiency with mRNA stability.

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Section: Discussionmentioning

confidence: 88%

The Ccr4-Not complex monitors the translating ribosome for codon optimality

Buschauer

Matsuo

Chen

et al. 2019

Preprint

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“…It is also possible that Tsr4 assembly with the N terminus of Rps2 itself is promoted by additional factors. The Ccr4-Not complex has recently been implicated in cotranslational assembly of the regulatory cap of the proteasome (44). Intriguingly, TSR4 was identified in a screen that also identified multiple components of the NOT complex, suggesting a functional link between Tsr4 and the Ccr4-Not complex (45).…”

Section: How Does Tsr4 Facilitate Rps2 Expression?mentioning

confidence: 99%

Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rps2 in Saccharomyces cerevisiae

Black

Musalgaonkar

Johnson

2019

Molecular and Cellular Biology

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Eukaryotic ribosome biogenesis requires the action of approximately 200 trans-acting factors and the incorporation of 79 ribosomal proteins (RPs). The delivery of RPs to preribosomes is a major challenge for the cell because RPs are often highly basic and contain intrinsically disordered regions prone to nonspecific interactions and aggregation. To counteract this, eukaryotes developed dedicated chaperones for certain RPs that promote their solubility and expression, often by binding eukaryote-specific extensions of the RPs. Rps2 (uS5) is a universally conserved RP that assembles into nuclear pre-40S subunits. However, a chaperone for Rps2 had not been identified. Our laboratory previously characterized Tsr4 as a 40S biogenesis factor of unknown function. Here, we report that Tsr4 cotranslationally associates with Rps2. Rps2 harbors a eukaryote-specific N-terminal extension that is critical for its interaction with Tsr4. Moreover, Tsr4 perturbation resulted in decreased Rps2 levels and phenocopied Rps2 depletion. Despite Rps2 joining nuclear pre-40S particles, Tsr4 appears to be restricted to the cytoplasm. Thus, we conclude that Tsr4 is a cytoplasmic chaperone dedicated to Rps2.

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“…2A-C). This data indicates that the co-translational assembly may not be strictly sequence-or site-specific 31,32 , but may originate from a more general mechanism; e.g. in a setting where protein subunits are brought into proximity during translation 33 .…”

Section: Discussionmentioning

confidence: 94%

Analysis of the co-translational assembly of the fungal fatty acid synthase (FAS)

Fischer

Joppe

Mulinacci

et al. 2020

Sci Rep

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The yeast fatty acid synthase (FAS) is a barrel-shaped 2.6 MDa complex. Upon barrel-formation, two multidomain subunits, each more than 200 kDa large, intertwine to form a heterododecameric complex that buries 170,000 Å 2 of protein surface. In spite of the rich knowledge about yeast FAS in structure and function, its assembly remained elusive until recently, when co-translational interaction of the β-subunit with the nascent α-subunit was found to initiate assembly. Here, we characterize the co-translational assembly of yeast FAS at a molecular level. We show that the co-translationally formed interface is sensitive to subtle perturbations, so that the exchange of two amino acids located in the emerging interface can prevent assembly. On the other hand, assembly can also be initiated via the co-translational interaction of the subunits at other sites, which implies that this process is not strictly site or sequence specific. We further highlight additional steps in the biogenesis of yeast FAS, as the formation of a dimeric subunit that orchestrates complex formation and acts as platform for post-translational phosphopantetheinylation. The presented data supports the understanding of the recently discovered prevalence of eukaryotic complexes for co-translational assembly, and is valuable for further harnessing FAS in the biotechnological production of aliphatic compounds. Fatty acid synthases (FAS) have been structurally studied during the last years, and a deep understanding about the molecular foundations of de novo fatty acid (FA) synthesis has been achieved 1-4 (Supplementary Fig. 1A,B). The architecture of fungal FAS was elucidated for the proteins from Saccharomyces cerevisiae (baker's yeast) 5-7 and the thermophilic fungus Thermomyces lanuginosus 8 , revealing an elaborate 2.6 MDa large α 6 β 6 barrel-shaped complex that encapsulates fungal de novo FA synthesis in its interior (Fig. 1A). The functional domains are embedded in a scaffolding matrix of multimerization and expansion elements. Acyl carrier protein (ACP) domains, shuttling substrates and intermediates inside the reaction chamber, achieve compartmentalized synthesis 5,9 (Fig. 1B,C). The concept of metabolic crowding makes fungal FAS a highly efficient machinery, running synthesis at micromolar virtual concentrations of active sites and substrates 10,11. The outstanding efficacy in fungal FA synthesis is documented by (engineered) oleagenic yeast that can grow to lipid cellular contents of up to 90% 12. Fungal FAS have also raised interest as biofactories in microbial production of value-added compounds from saturated carbon chains 13-15. Notwithstanding a profound knowledge about this protein family, the biogenesis of fungal FAS has not been investigated until recently, when Shiber et al. identified yeast FAS as initiating assembly via the co-translational interaction of subunits α (encoded by FAS2) and β (FAS1) 16. Co-translational assembly was analyzed with a modified version of a ribosome profiling protocol in which ribosome protected mRNA foo...

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Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes

Cited by 109 publications

References 59 publications

The Ccr4-Not complex monitors the translating ribosome for codon optimality

The Ccr4-Not complex monitors the translating ribosome for codon optimality

Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rps2 in Saccharomyces cerevisiae

Analysis of the co-translational assembly of the fungal fatty acid synthase (FAS)

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