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

ABSTRACT 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.

1 Follower
8 Reads
  • Source
    • "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. "
    [Show abstract] [Hide abstract]
    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
  • Source
    • "For example, 22 ubc genes are encoded in the C. elegans genome and we demonstrated that 4 genes, ubc-1, ubc-17, ubc-20, and ubc-21, could restrict intestinal cell cycles in the absence of ubc-25 activity. However, because the UBC-25/UBE2Q2-related proteins possess an amino-terminal extension that may confer unique regulatory or substrate specificities (Jones et al. 2002; Melner et al. 2006), it is not known whether these four genes acted interchangeably with ubc-25 or through a distinct compensatory mechanism. Second, the strict regulation of cell cycles is the collaborative result of independent pathways. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The development and homeostasis of multicellular animals requires precise coordination of cell division and differentiation. We performed a genome-wide RNAi screen in Caenorhabditis elegans to reveal the components of a regulatory network that promotes developmentally programmed cell-cycle quiescence. The 107 identified genes are predicted to constitute regulatory networks that are conserved among higher animals since almost half of the genes are represented by clear human orthologs. Using a series of mutant backgrounds to assess their genetic activities, the RNAi clones displaying similar properties were clustered to establish potential regulatory relationships within the network. This approach uncovered four distinct genetic pathways controlling cell-cycle entry during intestinal organogenesis. The enhanced phenotypes observed for animals carrying compound mutations attest to the collaboration between distinct mechanisms to ensure strict developmental regulation of cell cycles. Moreover, we characterized ubc-25, a gene encoding an E2 Ubiquitin conjugating enzyme whose human ortholog, UBE2Q2, is deregulated in several cancers. Our genetic analyses suggested that ubc-25 acts in a linear pathway with cul-1/Cul1, in parallel to pathways employing cki-1/p27 and lin-35/pRb to promote cell-cycle quiescence. Further investigation of the potential regulatory mechanism demonstrated that ubc-25 activity negatively regulates CYE-1/cyclin E protein abundance in vivo. Together, our results show that the ubc-25-mediated pathway acts within a complex network that integrates the actions of multiple molecular mechanisms to control cell cycles during development.
    G3-Genes Genomes Genetics 02/2014; 4(5). DOI:10.1534/g3.114.010546 · 3.20 Impact Factor
  • Source
    • "DEVELOPMENT multiple defects of larval development (Jones et al., 2002). In Drosophila, the semushi mutation of the ubc9 gene (lwr – FlyBase) causes multiple defects in anterior segmentation owing to misregulation of bicoid (Epps and Tanda, 1998). "
    [Show abstract] [Hide abstract]
    ABSTRACT: In vertebrates, establishment of the hematopoietic stem/progenitor cell (HSPC) pool involves mobilization of these cells in successive developmental hematopoietic niches. In zebrafish, HSPCs originate from the ventral wall of the dorsal aorta (VDA), the equivalent of the mammalian aorta-gonad-mesonephros (AGM). The HSPCs subsequently migrate to the caudal hematopoietic tissue (CHT) for transitory expansion and differentiation during the larval stage, and they finally colonize the kidney, where hematopoiesis takes place in adult fish. Here, we report the isolation and characterization of a zebrafish mutant, tango(hkz5), which shows defects of definitive hematopoiesis. In tango(hkz5) mutants, HSPCs initiate normally in the AGM and subsequently colonize the CHT. However, definitive hematopoiesis is not sustained in the CHT owing to accelerated apoptosis and diminished proliferation of HSPCs. Positional cloning reveals that tango(hkz5) encodes SUMO1-activating enzyme subunit 1 (Sae1). A chimera generation experiment and biochemistry analysis reveal that sae1 is cell-autonomously required for definitive hematopoiesis and that the tango(hkz5) mutation produces a truncated Sae1 protein (ΔSae1), resulting in systemic reduction of sumoylation. Our findings demonstrate that sae1 is essential for the maintenance of HSPCs during fetal hematopoiesis in zebrafish.
    Development 12/2012; 139(23):4321-9. DOI:10.1242/dev.081869 · 6.46 Impact Factor
Show more

Preview (2 Sources)

8 Reads
Available from