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

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Michael Zavortink ◽  
Lauren N Rutt ◽  
Svetlana Dzitoyeva ◽  
Jesslyn C Henriksen ◽  
Chloe Barrington ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Substrate Recognition ◽  
Ubiquitin Proteasome System ◽  
Structure Modeling ◽  
Animal Development ◽  
Maternal To Zygotic Transition ◽  
Ubiquitin Proteasome ◽  
Zygotic Genome

The maternal-to-zygotic transition (MZT) is a conserved step in animal development, where control is passed from the maternal to the zygotic genome. Although the MZT is typically considered from its impact on the transcriptome, we previously found that three maternally deposited Drosophila RNA-binding proteins (ME31B, Trailer Hitch [TRAL], and Cup) are also cleared during the MZT by unknown mechanisms. Here, we show that these proteins are degraded by the ubiquitin-proteasome system. Marie Kondo, an E2 conjugating enzyme, and the E3 CTLH ligase are required for the destruction of ME31B, TRAL, and Cup. Structure modeling of the Drosophila CTLH complex suggests that substrate recognition is different than orthologous complexes. Despite occurring hours earlier, egg activation mediates clearance of these proteins through the Pan Gu kinase, which stimulates translation of Kdo mRNA. Clearance of the maternal protein dowry thus appears to be a coordinated, but as-yet underappreciated, aspect of the MZT.

scholarly journals Egg activation triggers clearance of maternally deposited RNA binding proteins

2019 ◽  
Author(s):  
Michael Zavortink ◽  
Lauren N. Rutt ◽  
Svetlana Dzitoyeva ◽  
Chloe Barrington ◽  
Danielle Y. Bilodeau ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Ubiquitin Proteasome System ◽  
Egg Activation ◽  
List Type ◽  
Maternal Genome ◽  
Ubiquitin Conjugating Enzyme ◽  
Ubiquitin Proteasome ◽  
Conjugating Enzyme

SUMMARYThe maternal-to-zygotic transition (MZT) is a conserved step in animal development, where control is passed from the maternal genome to the zygotic one. Although the MZT is typically considered from its impact on the transcriptome, we previously found that three maternally deposited Drosophila RNA binding proteins (ME31B, Trailer Hitch [TRAL], and Cup) are also cleared during the MZT by unknown mechanisms. Here, we show that these proteins are degraded by the ubiquitin-proteasome system. Kondo, an E2 conjugating enzyme, and the E3 CTLH ligase are required for the destruction of ME31B, TRAL, and Cup. Importantly, despite occurring hours earlier, egg activation establishes the timer for clearance of these proteins by activating the Pan Gu kinase, which in turn stimulates translation of Kondo mRNA. In other words, egg activation triggers a series of regulatory events that culminate in the degradation of maternally deposited RNA binding proteins several hours later. Clearance of the maternal protein dowry thus appears to be a coordinated, but as-yet underappreciated, aspect of the MZT.HIGHLIGHTSDegradation of ME31B requires the PNG kinase, but not fertilizationThe ubiquitin-proteasome system degrades ME31B via CTLH E3 ligase and the UBC-E2H/Kondo ubiquitin-conjugating enzymeThe association of ME31B with the CTLH complex does not require PNG activityPNG kinase mediates the translational upregulation of Kondo at egg activation

scholarly journals Substrate Recognition and Specificity of Double-Stranded RNA Binding Proteins

Biochemistry ◽  
2014 ◽  
Vol 53 (21) ◽  
pp. 3457-3466 ◽  
Author(s):  
Lela Vuković ◽  
Hye Ran Koh ◽  
Sua Myong ◽  
Klaus Schulten
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Substrate Recognition ◽  
Double Stranded Rna

scholarly journals Substrate Recognition and Specificity of Double-Stranded RNA Binding Proteins

2014 ◽  
Vol 106 (2) ◽  
pp. 22a
Author(s):  
Lela Vukovic ◽  
Hye Ran Koh ◽  
Sua Myong ◽  
Klaus Schulten
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Substrate Recognition ◽  
Double Stranded Rna

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

2020 ◽  
Author(s):  
Michael Zavortink ◽  
Lauren N Rutt ◽  
Svetlana Dzitoyeva ◽  
Jesslyn C Henriksen ◽  
Chloe Barrington ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
E3 Ligase ◽  
Author Response ◽  
Maternal To Zygotic Transition

scholarly journals Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Vasiliy O. Sysoev ◽  
Bernd Fischer ◽  
Christian K. Frese ◽  
Ishaan Gupta ◽  
Jeroen Krijgsveld ◽  
...  
Keyword(s):  
Transcriptional Control ◽  
Rna Binding ◽  
Developmental Stages ◽  
Rna Binding Proteins ◽  
Global Changes ◽  
Maternal To Zygotic Transition ◽  
Capture Method ◽  
By Products ◽  
Insight Into ◽  
Zygotic Genome

AbstractThe maternal-to-zygotic transition (MZT) is a process that occurs in animal embryos at the earliest developmental stages, during which maternally deposited mRNAs and other molecules are degraded and replaced by products of the zygotic genome. The zygotic genome is not activated immediately upon fertilization, and in the pre-MZT embryo post-transcriptional control by RNA-binding proteins (RBPs) orchestrates the first steps of development. To identify relevant Drosophila RBPs organism-wide, we refined the RNA interactome capture method for comparative analysis of the pre- and post-MZT embryos. We determine 523 proteins as high-confidence RBPs, half of which were not previously reported to bind RNA. Comparison of the RNA interactomes of pre- and post-MZT embryos reveals high dynamicity of the RNA-bound proteome during early development, and suggests active regulation of RNA binding of some RBPs. This resource provides unprecedented insight into the system of RBPs that govern the earliest steps of Drosophila development.

scholarly journals Active protein neddylation or ubiquitylation is dispensable for stress granule dynamics

2018 ◽  
Author(s):  
Sebastian Markmiller ◽  
Amit Fulzele ◽  
Reneé Higgins ◽  
Gene W. Yeo ◽  
Eric J Bennett
Keyword(s):  
Protein Interactions ◽  
Sodium Arsenite ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Ubiquitin Proteasome System ◽  
Active Protein ◽  
Independent Manner ◽  
Ubiquitin Chain ◽  
Ubiquitin Pathway ◽  
Ubiquitin Proteasome

AbstractMany protein homeostasis stressors induce the formation of membraneless cytoplasmic stress granules (SGs) that contain large assemblies of repressed mRNAs and associated RNA binding proteins. Similar stressors have been shown to globally alter the function of the ubiquitin proteasome system (UPS) resulting in the accumulation of ubiquitylated proteins. Previous studies have demonstrated that ubiquitin and specific UPS components co-localize with SGs and that reducing the abundance or activity of ubiquitin pathway proteins can inhibit SG formation. These studies suggest that SG dynamics and composition may be regulated by ubiquitylation of SG resident proteins. Using ubiquitin-specific proteomic approaches, we demonstrate that many proteins, including some SG proteins are dynamically ubiquitylated upon SG-inducing sodium arsenite treatment. We utilized potent and selective inhibitors of the ubiquitin activating enzyme (UAE) or the NEDD8 activating enzyme (NAE) to directly test if active protein ubiquitylation or neddylation was required for SG dynamics. Using ubiquitin-site specific proteomics, we establish that UAE inhibition results in the rapid loss of nearly all protein ubiquitylation regardless of ubiquitin chain type. Addition of UAE or NAE inhibitors to cells did not alter arsenite-induced SG formation or dissolution. While we confirmed that ubiquitin co-localizes with both sodium arsenite and thapsigargin-induced SGs, antibodies that recognize all forms of ubiquitin more strongly co-localize with SGs compared to antibodies that preferentially recognize polyubiquitin or specific polyubiquitin-linkages. Interestingly, ubiquitin itself co-localizes with SGs in a UAE independent manner suggesting that the ubiquitin present within SGs is likely unconjugated ubiquitin. Our findings clearly demonstrate that active protein ubiquitylation or neddylation is not required for SG dynamics. These results suggest that ubiquitin-binding SG proteins may recruit free ubiquitin into SGs to modulate SG protein interactions.

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