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Query: UNIPROT:P62988 (Ubiquitin)
 4,326 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The polyubiquitin gene of the human protozoan parasite Plasmodium falciparum (PfpUB) was cloned and shown to be comprised of five tandem repeats of the ubiquitin open reading frame, present as a single copy on chromosome 12. The 1672 bp of PfpUB is interrupted at the 5' end by a single intron of 526 bp. PfpUB expression is developmentally regulated in intraerythrocytic stages with a marked increase in both steady-state transcript and polyubiquitin protein levels in late trophozoite stages. On response to heat shock, late stage parasites (late trophozoites and schizonts) have a slightly elevated PfpUB transcript level as well as readily observable increases in the amount of polyubiquitin and ubiquitin-conjugated proteins.
Mol Biochem Parasitol 2000 Jan 05
PMID:Intraerythrocytic polyubiquitin expression in Plasmodium falciparum is subjected to developmental and heat-shock control. 1061 4

Germline transformation of Drosophila melanogaster was attempted with the piggyBac gene-transfer system from the cabbage looper moth, Trichoplusia ni. Using a self-regulated transposase helper and a white marked vector, a transformation frequency of 1-3% per fertile G0 was obtained, similar to that previously achieved in the medfly. Use of an hsp70-regulated helper increased this frequency more than eight-fold. Transformation with a vector marked with white and green fluorescent protein (GFP) under polyubiquitin-nuclear localizing sequence regulation yielded seventy G1 transformants which all expressed GFP, but only twenty-seven of these expressed eye pigmentation that would have allowed their selection based on white+ expression. PiggyBac transformation in two distantly related dipteran species and efficient expression of the gfp marker supports the potential use of this system in other dipterans, and perhaps insects in general.
Insect Mol Biol 1999 Nov
PMID:Germline transformation of Drosophila melanogaster with the piggyBac transposon vector. 1063 70

We have isolated a polyubiquitin cDNA from the modified desiccation-tolerant grass Sporobolus stapfianus. This cDNA, along with a commercially available polyclonal ubiquitin antibody, was used to characterize desiccation/rehydrated-associated changes in ubiquitin-mediated protein degradation in S. stapfianus and the fully desiccation-tolerant moss Tortula ruralis. Northern analysis demonstrated that in S. stapfianus leaves two ubiquitin transcripts, of ca. 1.4 and 1.2 kb, accumulated above control levels during drying and rehydration but were barely detectable in desiccated tissue. The peak in rehydration-associated transcript accumulation coincided with a depletion in ubiquitin monomer levels indicating an increase in protein degradation. Analysis of T. ruralis revealed three ubiquitin transcripts of ca. 1.9, 1.3 and 0.65 kb, with only the 1.3 kb transcript level varying in response to drying and rehydration and all transcripts being stable in dried tissue. Western analysis revealed that conjugated ubiquitin, indicative of proteins targeted for removal, was evident in all samples of Sporobolus but detectable only in slow-drying Tortula which also displayed reduced levels of ubiquitin monomer. These results demonstrate that desiccated T. ruralis gametophyte possesses stable ubiquitin transcripts which can be translated upon rehydration enabling rapid initiation of cellular repair through degradation of certain proteins. This is in contrast to S. stapfianus which requires several hours to replenish depleted ubiquitin transcripts. The ubiquitin response to drying and rehydration in evolutionarily diverse systems is characterized, and the role of repair mechanisms such as ubiquitin-mediated protein degradation in desiccation tolerance is assessed.
Plant Mol Biol 1999 Nov
PMID:The involvement of ubiquitin in vegetative desiccation tolerance. 1064 25

We describe a purified ubiquitination system capable of rapidly catalyzing the covalent linkage of polyubiquitin chains onto a model substrate, phosphorylated IkappaBalpha. The initial ubiquitin transfer and subsequent polymerization steps of this reaction require the coordinated action of Cdc34 and the SCF(HOS/beta-TRCP)-ROC1 E3 ligase complex, comprised of four subunits (Skp1, cullin 1 [CUL1], HOS/beta-TRCP, and ROC1). Deletion analysis reveals that the N terminus of CUL1 is both necessary and sufficient for binding Skp1 but is devoid of ROC1-binding activity and, hence, is inactive in catalyzing ubiquitin ligation. Consistent with this, introduction of the N-terminal CUL1 polypeptide into cells blocks the tumor necrosis factor alpha-induced and SCF-mediated degradation of IkappaB by forming catalytically inactive complexes lacking ROC1. In contrast, the C terminus of CUL1 alone interacts with ROC1 through a region containing the cullin consensus domain, to form a complex fully active in supporting ubiquitin polymerization. These results suggest the mode of action of SCF-ROC1, where CUL1 serves as a dual-function molecule that recruits an F-box protein for substrate targeting through Skp1 at its N terminus, while the C terminus of CUL1 binds ROC1 to assemble a core ubiquitin ligase.
Mol Cell Biol 2000 Feb
PMID:The SCF(HOS/beta-TRCP)-ROC1 E3 ubiquitin ligase utilizes two distinct domains within CUL1 for substrate targeting and ubiquitin ligation. 1064 23

The ubiquitin-proteasome pathway, which is up-regulated in response to sensitizing treatments with serotonin (5-HT), plays a critical role in inducing long-term facilitation (LTF) of sensory-to-motor synapses in Aplysia. We characterized the structure of the polyubiquitin gene of Aplysia and studied its expression. At least six ubiquitin coding units exist in tandem, one of which encodes a protein with an amino acid sequence identical to human ubiquitin. Although the synthesis of polyubiquitin is induced by strong stimuli in many organisms, we found that the expression of ubiquitin in Aplysia is not affected by protocols that produce LTF.
Brain Res Mol Brain Res 2000 Mar 29
PMID:Structure and expression of the Aplysia polyubiquitin gene. 1076 22

Progression through mitosis requires the precisely timed ubiquitin-dependent degradation of specific substrates. E2-C is a ubiquitin-conjugating enzyme that plays a critical role with anaphase-promoting complex/cyclosome (APC/C) in progression of and exit from M phase. Here we report that mammalian E2-C is expressed in late G(2)/M phase and is degraded as cells exit from M phase. The mammalian E2-C shows an autoubiquitinating activity leading to covalent conjugation to itself with several ubiquitins. The ubiquitination of E2-C is strongly enhanced by APC/C, resulting in the formation of a polyubiquitin chain. The polyubiquitination of mammalian E2-C occurs only when cells exit from M phase. Furthermore, mammalian E2-C contains two putative destruction boxes that are believed to act as recognition motifs for APC/C. The mutation of this motif reduced the polyubiquitination of mammalian E2-C, resulting in its stabilization. These results suggest that mammalian E2-C is itself a substrate of the APC/C-dependent proteolysis machinery, and that the periodic expression of mammalian E2-C may be a novel autoregulatory system for the control of the APC/C activity and its substrate specificity.
Mol Biol Cell 2000 Aug
PMID:Cell cycle-dependent expression of mammalian E2-C regulated by the anaphase-promoting complex/cyclosome. 1093 Apr 72

Ubiquitin-specific processing proteases (UBPs) presently form the largest enzyme family in the ubiquitin system, characterized by a core region containing conserved motifs surrounded by divergent sequences, most commonly at the N-terminal end. The functions of these divergent sequences remain unclear. We identified two isoforms of a novel testis-specific UBP, UBP-t1 and UBP-t2, which contain identical core regions but distinct N termini, thereby permitting dissection of the functions of these two regions. Both isoforms were germ cell specific and developmentally regulated. Immunocytochemistry revealed that UBP-t1 was induced in step 16 to 19 spermatids while UBP-t2 was expressed in step 18 to 19 spermatids. Immunoelectron microscopy showed that UBP-t1 was found in the nucleus while UBP-t2 was extranuclear and was found in residual bodies. For the first time, we show that the differential subcellular localization was due to the distinct N-terminal sequences. When transfected into COS-7 cells, the core region was expressed throughout the cell but the UBP-t1 and UBP-t2 isoforms were concentrated in the nucleus and the perinuclear region, respectively. Fusions of each N-terminal end with green fluorescent protein yielded the same subcellular localization as the native proteins, indicating that the N-terminal ends were sufficient for determining differential localization. Interestingly, UBP-t2 colocalized with anti-gamma-tubulin immunoreactivity, indicating that like several other components of the ubiquitin system, a deubiquitinating enzyme is associated with the centrosome. Regulated expression and alternative N termini can confer specificity of UBP function by restricting its temporal and spatial loci of action.
Mol Cell Biol 2000 Sep
PMID:Divergent N-terminal sequences target an inducible testis deubiquitinating enzyme to distinct subcellular structures. 1093 31

The polyubiquitin gene, encoding tandemly repeated multiple ubiquitins, constitutes a uniquitin gene subfamily. It has been demonstrated that polyubiquitin genes are subject to concerted evolution; namely, the individual ubiquitin coding units contained within a polyubiquitin gene are more similar to one another than they are to the ubiquitin coding units in the orthologous gene from other species. However there has been no comprehensive study on the concerted evolution of polyubiquitin genes in a wide range of species, because the relationships (orthologous or paralogous) among multiple polyubiquitin genes from different species have not been extensively analyzed yet. In this report, we present the results of analyzing the nucleotide sequence of polyubiquitin genes of mammals, available in the DDBJ/EMBL/GenBank nucleotide sequence databases, in which we found that there are two groups of polyubiquitin genes in an orthologous relationship. Based on this result, we analyzed the concerted evolution of the polyubiquitin gene in various species and compared the frequency of concerted evolutionary events interspecifically by taking into consideration that the rate of synonymous substitution at the polyubiquitin gene locus may vary depending on species. We found that the concerted evolutionary events in polyubiquitin genes have been more frequent in rats and Chinese hamsters than those in humans, cows, and sheep. The guinea pig polyubiquitin gene was an intermediate example. The frequency of concerted evolution in the mouse gene was unexpectedly low compared to that of other rodent genes.
J Mol Evol 2000 Aug
PMID:Interspecific comparison in the frequency of concerted evolution at the polyubiquitin gene locus. 1094 72

A fully automatic procedure for predicting the amino acid sequences compatible with a given target structure is described. It is based on the CHARMM package, and uses an all atom force-field and rotamer libraries to describe and evaluate side-chain types and conformations. Sequences are ranked by a quantity akin to the free energy of folding, which incorporates hydration effects. Exact (Branch and Bound) and heuristic optimisation procedures are used to identifying highly scoring sequences from an astronomical number of possibilities. These sequences include the minimum free energy sequence, as well as all amino acid sequences whose free energy lies within a specified window from the minimum. Several applications of our procedure are illustrated. Prediction of side-chain conformations for a set of ten proteins yields results comparable to those of established side-chain placement programs. Applications to sequence optimisation comprise the re-design of the protein cores of c-Crk SH3 domain, the B1 domain of protein G and Ubiquitin, and of surface residues of the SH3 domain. In all calculations, no restrictions are imposed on the amino acid composition and identical parameter settings are used for core and surface residues. The best scoring sequences for the protein cores are virtually identical to wild-type. They feature no more than one to three mutations in a total of 11-16 variable positions. Tests suggest that this is due to the balance between various contributions in the force-field rather than to overwhelming influence from packing constraints. The effectiveness of our force-field is further supported by the sequence predictions for surface residues of the SH3 domain. More mutations are predicted than in the core, seemingly in order to optimise the network of complementary interactions between polar and charged groups. This appears to be an important energetic requirement in absence of the partner molecules with which the SH3 domain interacts, which were not included in the calculations. Finally, a detailed comparison between the sequences generated by the heuristic and exact optimisation algorithms, commends a note of caution concerning the efficiency of heuristic procedures in exploring sequence space.
J Mol Biol 2000 Aug 18
PMID:Automatic protein design with all atom force-fields by exact and heuristic optimization. 1096 79

The increase in the p53 activity in response to DNA damage is thought to be one of the important mechanisms by which p53 contributes to transcriptional activation of p21(wafl), mdm2, and other downstream regulatory genes. To investigate the p53 response to ultraviolet (UV) type of DNA damage, p53 protein level, its transcriptional activity and in vivo ubiquitination were compared in repair-proficient normal human fibroblasts (NHFs) and repair-deficient xeroderma pigmentosum (XP) group A and group C (XP-C) fibroblasts subsequent to irradiation with UV light. Accumulation of p53 protein level was observed with increasing UV doses in all the cell lines; however, discordance between p53 and p21(waf1) and mdm2 levels was observed in NHF and XP-A cells. Induction of p21(waf1) and mdm2 was inhibited by UV irradiation, requiring higher doses in NHF and lower doses in XP-A cells. However, inhibition of p21(waf1) and mdm2 induction was not observed in XP-C cells. Ubiquitin-p53 conjugates could be detected in irradiated or unirradiated NHF and XP-A cells but not in XP-C cells irradiated with 30 and 50 J/m(2) UV light. Using a p53 reporter assay, p53 transcriptional activities were found to be induced by 10 J/m(2) UV exposure and dramatically inhibited with increasing UV doses in NHF cells. Compared with repair-proficient NHF cells, UV inhibition of p53 transcriptional activity was relatively more sensitive in XP-A cells but resistant in XP-C cells. These results indicate that DNA damage by UV, in addition to inducing p53, acts as a trigger for inhibition of p53 transcriptional activity. Overall, recognition of DNA damage links both p53 induction and p53 degradation to DNA repair mechanisms.
Mol Carcinog 2000 Aug
PMID:Modulation of transcriptional activity of p53 by ultraviolet radiation: linkage between p53 pathway and DNA repair through damage recognition. 1097 91


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