The UBR-1 ubiquitin ligase regulates glutamate metabolism to generate coordinated motor pattern in Caenorhabditis elegans

AbstractUBR1 is an E3 ubiquitin ligase best known for its ability to target protein degradation by the N-end rule. The physiological functions of UBR family proteins, however, remain not fully understood. We found that the functional loss of C. elegans UBR-1 leads to a specific motor deficit: when adult animals generate reversal movements, A-class motor neurons exhibit synchronized activation, preventing body bending. This motor deficit is rescued by removing GOT-1, a transaminase that converts aspartate to glutamate. Both UBR-1 and GOT-1 are expressed and critically required in premotor interneurons of the reversal motor circuit to regulate the motor pattern. ubr-1 and got-1 mutants exhibit elevated and decreased glutamate level, respectively. These results raise an intriguing possibility that UBR proteins regulate glutamate metabolism, which is critical for neuronal development and signaling.Author SummaryUbiquitin-mediated protein degradation is central to diverse biological processes. The selection of substrates for degradation is carried out by the E3 ubiquitin ligases, which target specific groups of proteins for ubiquitination. The human genome encodes hundreds of E3 ligases; many exhibit sequence conservation across animal species, including one such ligase called UBR1. Patients carrying mutations in UBR1 exhibit severe systemic defects, but the biology behinds UBR1’s physiological function remains elusive. Here we found that the C. elegans UBR-1 regulates glutamate level. When UBR-1 is defective, C. elegans exhibits increased glutamate; this leads to synchronization of motor neuron activity, hence defective locomotion when animals reach adulthood. UBR1-mediated glutamate metabolism may contribute to the physiological defects of UBR1 mutations.

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The Caenorhabditis elegans Replication Licensing Factor CDT-1 Is Targeted for Degradation by the CUL-4/DDB-1 Complex

Molecular and Cellular Biology ◽

10.1128/mcb.00736-06 ◽

2006 ◽

Vol 27 (4) ◽

pp. 1394-1406 ◽

Cited By ~ 35

Author(s):

Youngjo Kim ◽

Edward T. Kipreos

Keyword(s):

Caenorhabditis Elegans ◽

Ubiquitin Ligase ◽

S Phase ◽

Null Mutant ◽

Wild Type ◽

C Elegans ◽

Licensing Factor ◽

Ubiquitin Ligase E3 ◽

Blast Cells ◽

Temporal Restriction

ABSTRACT The replication of genomic DNA is strictly regulated to occur only once per cell cycle. This regulation centers on the temporal restriction of replication licensing factor activity. Two distinct ubiquitin ligase (E3) complexes, CUL4/DDB1 and SCFSkp2, have been reported to target the replication licensing factor Cdt1 for ubiquitin-mediated proteolysis. However, it is unclear to what extent these two distinct Cdt1 degradation pathways are conserved. Here, we show that Caenorhabditis elegans DDB-1 is required for the degradation of CDT-1 during S phase. DDB-1 interacts specifically with CUL-4 but not with other C. elegans cullins. A ddb-1 null mutant exhibits extensive DNA rereplication in postembryonic BLAST cells, similar to what is observed in cul-4(RNAi) larvae. DDB-1 physically associates with CDT-1, suggesting that CDT-1 is a direct substrate of the CUL-4/DDB-1 E3 complex. In contrast, a deletion mutant of the C. elegans Skp2 ortholog, skpt-1, appears overtly wild type with the exception of an impenetrant gonad migration defect. There is no appreciable role for SKPT-1 in the degradation of CDT-1 during S phase, even in a sensitized ddb-1 mutant background. We propose that the CUL-4/DDB-1 ubiquitin ligase is the principal E3 for regulating the extent of DNA replication in C. elegans.

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ER E3 ubiquitin ligase HRD-1 and its specific partner chaperone BiP play important roles in ERAD and developmental growth in Caenorhabditis elegans

Genes to Cells ◽

10.1111/j.1365-2443.2007.01108.x ◽

2007 ◽

Vol 12 (9) ◽

pp. 1063-1073 ◽

Cited By ~ 32

Author(s):

Yohei Sasagawa ◽

Kunitoshi Yamanaka ◽

Teru Ogura

Keyword(s):

Caenorhabditis Elegans ◽

Ubiquitin Ligase ◽

E3 Ubiquitin Ligase ◽

Developmental Growth

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Ubiquitin ligases and a processive proteasome facilitate protein clearance during the oocyte-to-embryo transition in Caenorhabditis elegans

10.1101/2021.11.05.467479 ◽

2021 ◽

Author(s):

Caroline A. Spike ◽

Tatsuya Tsukamoto ◽

David Greenstein

Keyword(s):

Caenorhabditis Elegans ◽

Ubiquitin Ligase ◽

Rna Binding ◽

Rna Binding Proteins ◽

Regulatory Proteins ◽

Critical Determinant ◽

C Elegans ◽

Protein Clearance ◽

M Phase ◽

F Box Protein

The ubiquitin-mediated degradation of oocyte translational regulatory proteins is a conserved feature of the oocyte-to-embryo transition (OET). In the nematode Caenorhabditis elegans, multiple translational regulatory proteins, including the TRIM-NHL RNA-binding protein LIN-41/Trim71 and the Pumilio-family RNA-binding proteins PUF-3 and PUF-11, are degraded during the OET. Degradation of each protein requires activation of the M-phase cyclin-dependent kinase CDK-1, is largely complete by the end of the first meiotic division and does not require the anaphase promoting complex (APC). However, only LIN-41 degradation requires the F-box protein SEL-10/FBW7/Cdc4p, the substrate recognition subunit of an SCF-type E3 ubiquitin ligase. This finding suggests that PUF-3 and PUF-11, which localize to LIN-41-containing ribonucleoprotein particles (RNPs), are independently degraded through the action of other factors and that the oocyte RNPs are disassembled in a concerted fashion during the OET. We develop and test the hypothesis that PUF-3 and PUF-11 are targeted for degradation by the proteasome-associated HECT-type ubiquitin ligase ETC-1/UBE3C/Hul5, which is broadly expressed in C. elegans. We find that several GFP-tagged fusion proteins that are degraded during the OET, including fusions with PUF-3, PUF-11, LIN-41, IFY-1/Securin and CYB-1/Cyclin B, are incompletely degraded when ETC-1 function is compromised. However, it is the fused GFP moiety that appears to be the critical determinant of this proteolysis defect. These findings are consistent with a conserved role for ETC-1 in promoting proteasome processivity and suggest that proteasomal processivity is an important element of the OET during which many key oocyte regulatory proteins are rapidly targeted for degradation.

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Mitotic replisome disassembly depends on TRAIP ubiquitin ligase activity

Life Science Alliance ◽

10.26508/lsa.201900390 ◽

2019 ◽

Vol 2 (2) ◽

pp. e201900390 ◽

Cited By ~ 12

Author(s):

Sara Priego Moreno ◽

Rebecca M Jones ◽

Divyasree Poovathumkadavil ◽

Shaun Scaramuzza ◽

Agnieszka Gambus

Keyword(s):

Caenorhabditis Elegans ◽

Xenopus Laevis ◽

Ubiquitin Ligase ◽

S Phase ◽

Replication Forks ◽

Replication Machinery ◽

Replicative Helicase ◽

Egg Extract ◽

Ubiquitin Ligase Activity ◽

Mitotic Chromatin

We have shown previously that the process of replication machinery (replisome) disassembly at the termination of DNA replication forks in the S-phase is driven through polyubiquitylation of one of the replicative helicase subunits (Mcm7) by Cul2LRR1 ubiquitin ligase. Interestingly, upon inhibition of this pathway in Caenorhabditis elegans embryos, the replisomes retained on chromatin were unloaded in the subsequent mitosis. Here, we show that this mitotic replisome disassembly pathway exists in Xenopus laevis egg extract and we determine the first elements of its regulation. The mitotic disassembly pathway depends on the formation of K6- and K63-linked ubiquitin chains on Mcm7 by TRAIP ubiquitin ligase and the activity of p97/VCP protein segregase. Unlike in lower eukaryotes, however, it does not require SUMO modifications. Importantly, we also show that this process can remove all replisomes from mitotic chromatin, including stalled ones, which indicates a wide application for this pathway over being just a “backup” for terminated replisomes. Finally, we characterise the composition of the replisome retained on chromatin until mitosis.

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APC/CFZR-1 Controls ZYG-1 Levels to Regulate Centrosome Assembly

10.1101/2020.08.12.248658 ◽

2020 ◽

Author(s):

Jeffrey C. Medley ◽

Joseph R. DiPanni ◽

Luke Schira ◽

Blake M. Shaffou ◽

Brandon M. Sebou ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Ubiquitin Ligase ◽

Threshold Level ◽

Anaphase Promoting Complex ◽

Tight Control ◽

C Elegans ◽

Protein Levels ◽

Bipolar Spindles ◽

Embryonic Viability ◽

Centrosome Protein

AbstractAberrant centrosome numbers are associated with human cancers. The levels of centrosome regulators positively correlate with centrosome number. Thus, tight control of centrosome protein levels is critical. In Caenorhabditis elegans, the anaphase-promoting complex/cyclosome and co-activator FZR-1 (APC/CFZR-1) ubiquitin ligase negatively regulates centrosome assembly through SAS-5 degradation. In this study, we identify the C. elegans ZYG-1 (Plk4 in human) as a new substrate of APC/CFZR-1. Inhibiting APC/CFZR-1 or mutating a ZYG-1 destruction (D)-box leads to elevated ZYG-1 levels at centrosomes, restoring bipolar spindles and embryonic viability to zyg-1 mutants, suggesting that APC/CFZR-1 targets ZYG-1 for proteasomal degradation via D-box motif. We also show the Slimb/βTrCP-binding (SB) motif is critical for ZYG-1 degradation, substantiating a conserved mechanism by which ZYG-1/Plk4 stability is regulated by SCFSlimb/βTrCP-dependent proteolysis via the conserved SB motif in C. elegans. Furthermore, inhibiting both APC/CFZR-1 and SCFSlimb/βTrCP, by co-mutating ZYG-1 SB and D-box motifs, stabilizes ZYG-1 in an additive manner, conveying that APC/CFZR-1 and SCFSlimb/βTrCP ubiquitin ligases function cooperatively for timely ZYG-1 destruction in C. elegans embryos where ZYG-1 activity remains at threshold level to ensure normal centrosome number.

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LIN-23, an E3 Ubiquitin Ligase Component, Is Required for the Repression of CDC-25.2 Activity during Intestinal Development in Caenorhabditis elegans

Molecules and Cells ◽

10.14348/molcells.2016.0238 ◽

2016 ◽

Vol 39 (11) ◽

pp. 834-840 ◽

Cited By ~ 2

Author(s):

Miseol Son ◽

Ichiro Kawasaki ◽

Bong-Kyeong Oh ◽

Yhong-Hee Shim

Keyword(s):

Caenorhabditis Elegans ◽

Ubiquitin Ligase ◽

E3 Ubiquitin Ligase ◽

Intestinal Development

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KEL-8 Is a Substrate Receptor for CUL3-dependent Ubiquitin Ligase That Regulates Synaptic Glutamate Receptor Turnover

Molecular Biology of the Cell ◽

10.1091/mbc.e05-08-0794 ◽

2006 ◽

Vol 17 (3) ◽

pp. 1250-1260 ◽

Cited By ~ 56

Author(s):

Henry Schaefer ◽

Christopher Rongo

Keyword(s):

Caenorhabditis Elegans ◽

Glutamate Receptors ◽

Propionic Acid ◽

Glutamate Receptor ◽

Ubiquitin Ligase ◽

Ubiquitin Ligases ◽

Synaptic Proteins ◽

Neuronal Protein ◽

Cullin 3 ◽

Receptor Turnover

The regulated localization of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type glutamate receptors (AMPARs) to synapses is an important component of synaptic signaling and plasticity. Regulated ubiquitination and endocytosis determine the synaptic levels of AMPARs, but it is unclear which factors conduct these processes. To identify genes that regulate AMPAR synaptic abundance, we screened for mutants that accumulate high synaptic levels of the AMPAR subunit GLR-1 in Caenorhabditis elegans. GLR-1 is localized to postsynaptic clusters, and mutants for the BTB-Kelch protein KEL-8 have increased GLR-1 levels at clusters, whereas the levels and localization of other synaptic proteins seem normal. KEL-8 is a neuronal protein and is localized to sites adjacent to GLR-1 postsynaptic clusters along the ventral cord neurites. KEL-8 is required for the ubiquitin-mediated turnover of GLR-1 subunits, and kel-8 mutants show an increased frequency of spontaneous reversals in locomotion, suggesting increased levels of GLR-1 are present at synapses. KEL-8 binds to CUL-3, a Cullin 3 ubiquitin ligase subunit that we also find mediates GLR-1 turnover. Our findings indicate that KEL-8 is a substrate receptor for Cullin 3 ubiquitin ligases that is required for the proteolysis of GLR-1 receptors and suggest a novel postmitotic role in neurons for Kelch/CUL3 ubiquitin ligases.

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