The E2 Marie Kondo and the CTLH E3 ligase clear deposited RNA binding proteins during the maternal-to-zygotic transition

Zavortink, Michael; Rutt, Lauren N.; Dzitoyeva, Svetlana; Henriksen, Jesslyn C; Barrington, Chloe; Bilodeau, Danielle Y; Wang, Miranda; Chen, Xiao Xiao; Rissland, Olivia S.

doi:10.7554/elife.53889

Cited by 35 publications

(55 citation statements)

References 50 publications

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“…While the role of the GID ligase in the regulation of gluconeogenesis is well-characterized, the conservation of this multiprotein complex throughout eukaryotes suggests that it likely regulates additional pathways. For example, the GID/CTLH complex has a role in erythropoiesis and spermatogenesis in human cells and in embryogenesis in Drosophila ( 62 – 65 ). Thus, we set out to uncover additional pathways regulated by the GID E3 ligase in yeast by utilizing a combination of mutants.…”

Section: Resultsmentioning

confidence: 99%

“…However, Gid4, while conserved in human cells, is not conserved throughout all eukaryotes. For example, the GID complex in Drosophila lacks an identifiable Gid4 homolog ( 65 ), suggesting an alternate mode of recognition. In addition, in yeast, the protein Gid10 has been identified as an alternate substrate receptor of the GID complex ( 40 , 67 ), although no Gid10-dependent cellular substrates have been identified to date.…”

Section: Resultsmentioning

confidence: 99%

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DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift

Karayel

Michaelis

Mann

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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The yeastSaccharomyces cerevisiaeis a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run, data-independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement, and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source-dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system readout pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation of targets of the GID E3 ligase. Moreover, this approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole-proteome–based readouts can serve as comprehensive systems-level assays in all cellular systems.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift

Karayel

Michaelis

Mann

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…Physiological importance of the CTLH E3 is underscored by developmental defects in flies, fish, frogs, and mammals arising from genetic deletions or mutations of its subunits (Han et al, 2016;Javan et al, 2018;Nguyen et al, 2017;Pfirrmann et al, 2015;Soni et al, 2006;Wei et al, 2019;Zavortink et al, 2020;Zhen et al, 2020). Yet, how Gid7 or its human orthologs regulate GID and CTLH E3 ligase complexes is unknown.…”

Section: Introductionmentioning

confidence: 99%

GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme

Sherpa¹,

Chrustowicz²,

Qiao³

et al. 2021

Preprint

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To achieve precise cellular regulation, E3 ubiquitin ligases must be configured to match substrate quaternary structures. Here, by studying the yeast GID complex, mutation of which is Glucose-Induced Degradation deficient, we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryo EM structures show that to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two otherwise functional GID E3s assemble into a 20-protein Chelator-GIDSR4, which resembles an organometallic supramolecular chelate. The Chelator-GIDSR4 assembly avidly binds multiple Fbp1 degrons and positions Fbp1 so that its protomers are simultaneously ubiquitylated at lysines near its allosteric and substrate binding sites. Significantly, key structural and biochemical features - including capacity for supramolecular assembly - are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical and cell biological data, we propose that higher-order E3 ligase assembly generally underlies multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.

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“…It also remains to be tested whether CG5003 has additional roles later than the observed arrest in the early embryonic divisions, perhaps in maternal proteome clearance after zygotic genome activation. A precedent for this derives from a recent study that identified an E2 and an E3 ligase responsible for the degradation of maternal RNA binding proteins at the maternal-to-zygotic transition (Zavortink et al 2020). Experiments addressing the diversity of E3 ubiquitin complexes and the subsets of targets under their regulation in early embryos should yield new insights into proteome remodeling during embryogenesis.…”

Section: Discussionmentioning

confidence: 99%

Identification of New Regulators of the Oocyte-to-Embryo Transition inDrosophila

Avilés-Pagán

Kang

Orr‐Weaver

2020

G3 Genes|Genomes|Genetics

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At the oocyte-to-embryo transition the highly differentiated oocyte arrested in meiosis becomes a totipotent embryo capable of embryogenesis. Oocyte maturation (release of the prophase I primary arrest) and egg activation (release from the secondary meiotic arrest and the trigger for the oocyte-to-embryo transition) serve as prerequisites for this transition, both events being controlled posttranscriptionally. Recently, we obtained a comprehensive list of proteins whose levels are developmentally regulated during these events via a high-throughput quantitative proteomic analysis of Drosophila melanogaster oocyte maturation and egg activation. We conducted a targeted screen for potential novel regulators of the oocyte-to-embryo transition, selecting 53 candidates from these proteins. We reduced the function of each candidate gene using transposable element insertion alleles and RNAi, and screened for defects in oocyte maturation or early embryogenesis. Deletion of the aquaporin gene CG7777 did not affect female fertility. However, we identified CG5003 and nebu (CG10960) as new regulators of the transition from oocyte to embryo. Mutations in CG5003, which encodes an F-box protein associated with SCF-proteasome degradation function, cause a decrease in female fertility and early embryonic arrest. Mutations in nebu, encoding a putative glucose transporter, result in defects during the early embryonic divisions, as well as a developmental delay and arrest. nebu mutants also exhibit a defect in glycogen accumulation during late oogenesis. Our findings highlight potential previously unknown roles for the ubiquitin protein degradation pathway and sugar transport across membranes during this time, and paint a broader picture of the underlying requirements of the oocyte-to-embryo transition.

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The E2 Marie Kondo and the CTLH E3 ligase clear deposited RNA binding proteins during the maternal-to-zygotic transition

Cited by 35 publications

References 50 publications

DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift

DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift

GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme

Identification of New Regulators of the Oocyte-to-Embryo Transition inDrosophila

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