Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: Ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins

Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver V6T 1Z3, Canada.
Genome biology (Impact Factor: 10.81). 02/2002; 3(1):RESEARCH0002. DOI: 10.1186/gb-2001-3-1-research0002
Source: PubMed


The eukaryotic ubiquitin-conjugation system sets the turnover rate of many proteins and includes activating enzymes (E1s), conjugating enzymes (UBCs/E2s), and ubiquitin-protein ligases (E3s), which are responsible for activation, covalent attachment and substrate recognition, respectively. There are also ubiquitin-like proteins with distinct functions, which require their own E1s and E2s for attachment. We describe the results of RNA interference (RNAi) experiments on the E1s, UBC/E2s and ubiquitin-like proteins in Caenorhabditis elegans. We also present a phylogenetic analysis of UBCs.
The C. elegans genome encodes 20 UBCs and three ubiquitin E2 variant proteins. RNAi shows that only four UBCs are essential for embryogenesis: LET-70 (UBC-2), a functional homolog of yeast Ubc4/5p, UBC-9, an ortholog of yeast Ubc9p, which transfers the ubiquitin-like modifier SUMO, UBC-12, an ortholog of yeast Ubc12p, which transfers the ubiquitin-like modifier Rub1/Nedd8, and UBC-14, an ortholog of Drosophila Courtless. RNAi of ubc-20, an ortholog of yeast UBC1, results in a low frequency of arrested larval development. A phylogenetic analysis of C. elegans, Drosophila and human UBCs shows that this protein family can be divided into 18 groups, 13 of which include members from all three species. The activating enzymes and the ubiquitin-like proteins NED-8 and SUMO are required for embryogenesis.
The number of UBC genes appears to increase with developmental complexity, and our results suggest functional overlap in many of these enzymes. The ubiquitin-like proteins NED-8 and SUMO and their corresponding activating enzymes are required for embryogenesis.

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    • "Ortholog of human kelch-like family member 18 kel-3 protein F15D3.5, the ubiquitin-conjugating enzyme UBC-20 (Jones et al., 2002), the glutathione-s-transferase GST-36, and a protein with homology to calmodulin CAL-4. "
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    ABSTRACT: To expand the understanding of aging in the model organism Caenorhabditis elegans, global quantification of metabolite and protein levels in young and aged nematodes was performed using mass spectrometry. With age, there was a decreased abundance of proteins functioning in transcription termination, mRNA degradation, mRNA stability, protein synthesis, and proteasomal function. Furthermore, there was altered S-adenosyl methionine metabolism as well as a decreased abundance of the S-adenosyl methionine synthetase (SAMS-1) protein. Other aging-related changes included alterations in free fatty acid levels and composition, decreased levels of ribosomal proteins, decreased levels of NADP-dependent isocitrate dehydrogenase (IDH1), a shift in the cellular redox state, an increase in sorbitol content, alterations in free amino acid levels, and indications of altered muscle function and sarcoplasmic reticulum Ca(2+) homeostasis. There were also decreases in pyrimidine and purine metabolite levels, most markedly nitrogenous bases. Supplementing the culture medium with cytidine (a pyrimidine nucleoside) or hypoxanthine (a purine base) increased lifespan slightly, suggesting that aging-induced alterations in ribonucleotide metabolism affect lifespan. An age-related increase in body size, lipotoxicity from ectopic yolk lipoprotein accumulation, a decline in NAD(+) levels, and mitochondrial electron transport chain dysfunction may explain many of these changes. In addition, dietary restriction in aged worms resulting from sarcopenia of the pharyngeal pump likely decreases the abundance of SAMS-1, possibly leading to decreased phosphatidylcholine levels, larger lipid droplets, and ER and mitochondrial stress. The complementary use of proteomics and metabolomics yielded unique insights into the molecular processes altered with age in C. elegans.
    Experimental gerontology 09/2015; 72. DOI:10.1016/j.exger.2015.09.013 · 3.49 Impact Factor
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    • "Class I only possesses the catalytic core/Ubiquitin Conjugating (Ubc fold) domain, class II and III have N-or C-terminal extensions respectively and class IV possesses both. Classification of E2s is still debated as they are grouped in 17–18 families depending on authors (Jones et al., 2002; Michelle et al., 2009). For easiest comprehension we will refer in this manuscript to the current nomenclature (UBE2x) with x defining each individual E2 enzyme. "
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    ABSTRACT: The Ubiquitin Proteasome System (UPS) is a major actor of muscle wasting during various physio-pathological situations. In the past 15 years, increasing amounts of data have depicted a picture, although incomplete, of the mechanisms implicated in myofibrillar protein degradation, from the discovery of muscle-specific E3 ligases to the identification of the signaling pathways involved. The targeting specificity of the UPS relies on the capacity of the system to first recognize and then label the proteins to be degraded with a poly-ubiquitin (Ub) chain. It is fairly assumed that the recognition of the substrate is accomplished by the numerous E3 ligases present in mammalian cells. However, most E3s do not possess any catalytic activity and E2 enzymes may be more than simple Ub-providers for E3s since they are probably important actors in the ubiquitination machinery. Surprisingly, most authors have tried to characterize E3 substrates, but the exact role of E2s in muscle protein degradation is largely unknown. A very limited number of the 35 E2s described in humans have been studied in muscle protein breakdown experiments and the vast majority of studies were only descriptive. We review here the role of E2 enzymes in skeletal muscle and the difficulties linked to their study and provide future directions for the identification of muscle E2s responsible for the ubiquitination of contractile proteins.
    Frontiers in Physiology 03/2015; 6:59. DOI:10.3389/fphys.2015.00059 · 3.53 Impact Factor
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    • "dtke et al . , 2005 ; Yu et al . , 2012 ) . The existence of a mechanism that regulates the precise interplay between the FANC and neddylation pathways is supported not only by the findings from our present study but also by several published observations . NEDD8 target proteins are involved in chromatin remodeling and DNA repair and replication ( Jones et al . , 2002 ; Xirodimas , 2008 ) , in which the FANC pathway is also involved . Inhibition of neddylation increases both CHK1 stability and the activation of the G2 / M checkpoint ( Yang et al . , 2012 ) , which are two important cellular features associated with Fanconi anemia ( Guervilly et al . , 2011 ) . Additionally , neddylation negatively re"
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    ABSTRACT: The aim of this study was to identify novel substrates of the FANCcore complex, which inactivation leads to the genetic disorder Fanconi anemia (FA), which associates bone marrow failure, developmental abnormalities and predisposition to cancer. Eight FANC proteins participate in the nuclear FANCcore complex, an E3 ubiquitin-ligase that monoubiquitinates FANCD2 and FANCI in response to replicative stress. Here, we used mass spectrometry to compare proteins from FANCcore complex deficient FA-A and FA-C cells to their ectopically corrected counterparts challenged with hydroxyurea, an inducer of FANCD2 monoubiquitination. FANCD2 and FANCI appear as the only targets of the FANCcore complex. We identified other proteins post-translationally modified in a FANCA- or FANCC-dependent manner. The majority of these potential targets localizes to the cell membrane. Finally, we demonstrated that (a) the chemokine receptor CXCR5 is neddylated; (b) FANCA, but not FANCC, appears to modulate CXCR5 neddylation through an unknown mechanism; (c) CXCR5 neddylation is involved in targeting the receptor to the cell membrane; and (d) CXCR5 neddylation stimulates cell migration/motility. Our work has uncovered a pathway involving FANCA in neddylation and cell motility.
    Journal of Cell Science 07/2014; 127(16). DOI:10.1242/jcs.150706 · 5.43 Impact Factor
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