A specialised
            <scp>SKI</scp>
            complex assists the cytoplasmic
            <scp>RNA</scp>
            exosome in the absence of direct association with ribosomes

Zhang, Elodie; Khanna, Varun; Dacheux, Estelle; Namane, Abdelkader; Doyen, Antonia; Gomard, Maïté; Turcotte, Bernard; Jacquier, Alain; Fromont‐Racine, Micheline

doi:10.15252/embj.2018100640

Cited by 27 publications

(28 citation statements)

References 39 publications

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“…A BY4741 strain containing genomic TAP-tagged SKI3 and a plasmid overexpressing SKA1 (pCM190) (Zhang et al, 2019) was used for generation of the cryo-EM sample.…”

Section: Preparation Of Native Yeast 40s Complexesmentioning

confidence: 99%

Structural inventory of native ribosomal ABCE1-43S pre-initiation complexes

Kratzat

Mackens-Kiani

Ameismeier

et al. 2020

Preprint

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In eukaryotic translation, the termination and recycling phases are linked to subsequent initiation by persistence of several factors. These comprise the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP-binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of 43S pre-initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1-containing pre-initiation complexes by cryo-EM. We found that ABCE1 was mostly associated with early 43S but also later 48S phases of initiation. It directly interacted with eIF3j via its unique iron-sulfur cluster domain and adopted a novel hybrid conformation, which was ATPase-inhibited and stabilized by an unknown factor bound between the nucleotide binding sites. Moreover, the native human samples provided a near-complete molecular picture of the architecture and sophisticated interaction network of the 43S-bound eIF3 complex and also the eIF2 ternary complex containing the initiator tRNA.

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“…A BY4741 strain containing genomic TAP-tagged SKI3 and a plasmid overexpressing SKA1 (pCM190) (Zhang et al, 2019) was used for generation of the cryo-EM sample.…”

Section: Preparation Of Native Yeast 40s Complexesmentioning

confidence: 99%

Structural inventory of native ribosomal ABCE1-43S pre-initiation complexes

Kratzat

Mackens-Kiani

Ameismeier

et al. 2020

Preprint

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“…Thus, for example, the DAmP modification of the 3' to 5' RNA degradation exosome complex component RRP46, and of the rRNA modification complex component NOP56 were synthetic sick with the deletion of several RNA-related genes ( Fig. 4 -figure supplement 1), including the poorly characterized locus YCL001W-A and the recently identified SKI complex associated protein Ska1 (Zhang et al, 2019). Altogether, these results illustrate the value of including mutants of essential genes in GIM screens.…”

Section: The Amplitude Of Gis For Damp Alleles Correlates With Specifmentioning

confidence: 61%

“…The corresponding protein has similarity with a region of DOM34, a protein involved in ribosome dissociation and RNA degradation during no-go decay. SKA1, whose deletion was synthetic sick with nop56-DAmP was recently described to have a role in the 3' to 5' degradation of RNAs(Zhang et al, 2019).…”

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confidence: 99%

Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast

Decourty

Malabat

Frachon

et al. 2020

Preprint

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Gene deletion and gene expression alteration can lead to growth defects that are amplified or reduced when a second mutation is present in the same cells. We performed 154 genetic interaction mapping (GIM) screens with mutants related with RNA metabolism and measured growth rates of about 700 000 Saccharomyces cerevisiae double mutant strains. The screens used the gene deletion collection in addition to a set of 900 strains in which essential genes were affected by mRNA destabilization (DAmP). To analyze the results we developed RECAP, a strategy that validates genetic interaction profiles by comparison with gene co-citation frequency, and identified links between 1 471 genes and 117 biological processes. To validate specific results, we tested and confirmed a link between an inositol polyphosphate hydrolase complex and mRNA translation initiation. Altogether, the results and the newly developed analysis strategy should represent a useful resource for discovery of gene function in yeast.

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“…Of the others, SKA1 encodes a protein proposed to facilitate exosome (3'-5' exonuclease) function in the catabolism of non-ribosome-associated mRNAs 65 , while YGR016W encodes a protein of unknown function. While the connection of these proteins to the negative regulation of mating is unknown, both proteins were shown to be substrates of the E3 ubiquitin ligase, Rsp5 66 .…”

Section: Categorization Of Chemotropism Mutantsmentioning

confidence: 99%

Translational control as a novel regulator of gradient sensing and chemotropism in yeast

Gelin-Licht

Conlon

Singh

et al. 2020

Preprint

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The yeast mating pathway regulates haploid cell fusion to form diploids in response to pheromone signaling. Study of this pathway has led to important insights into the structure and function of mitogen-activated protein kinase (MAPK) cascades, yet our understanding of how external signals are converted into specific changes in gene expression and cell morphology is incomplete. For example, the regulators of directional growth (chemotropism) remain poorly defined. Upon pheromone exposure, yeast grow asymmetrically towards a nearby mating partner (chemotropic morphogenesis) and form a mating projection (shmoo). Using non-biased genome-wide screening, we identify >20 novel positive and negative regulators of pheromone gradient sensing, shmoo development, and mating. In addition to known regulators of exocytic and endocytic pathways, several are directly involved in translational control downstream of the G-protein-regulated pheromone and filamentous growth MAPK pathways. These include the Scp160 RNA-binding protein and ribosomal proteins Asc1, Rpl12b and Rpl19b. Importantly, pheromone treatment and Gα (Gpa1) activation both stimulate Scp160 binding to, and inhibition of, Asc1, which acts downstream of glucose-activated Gα (Gpa2) on the filamentous growth pathway. We also identify Rpl12b and Rpl19b as paralog-specific positive regulators of translation of specific mating pathway components, including Scp160. Thus, the different MAPK pathways converge at the level of translational control to regulate signaling.

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A specialised SKI complex assists the cytoplasmic RNA exosome in the absence of direct association with ribosomes

Cited by 27 publications

References 39 publications

Structural inventory of native ribosomal ABCE1-43S pre-initiation complexes

Structural inventory of native ribosomal ABCE1-43S pre-initiation complexes

Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast

Translational control as a novel regulator of gradient sensing and chemotropism in yeast

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