The ubiquitin system: functions and mechanisms

Antigenic characteristics of neurofibrillary tangles in progressive supranuclear palsy

The antigenic components of neurofibrillary tangles in the basal forebrain and brainstem were studied in 4 cases of progressive supranuclear palsy (PSP) at the light and electron microscopic levels, using antibodies to neurofilaments (in the phosphorylated and non-phosphorylated forms); the high, middle and low molecular weight neurofilament subunits; ubiquitin; the microtubule associated proteins MAP1, MAP2 and tau; isolated Alzheimer paired helical filaments and to tubulin, in the tyrosinated and detyrosinated forms. Although PSP neurofibrillary tangles appear to have most antigenic sites in common with those of Alzheimer disease, PSP tangles share epitopes with tyrosinated and detyrosinated tubulin, which has not been demonstrated in Alzheimer neurofibrillary tangles.

Characterization of a polyubiquitin gene from Arabidopsis thaliana

Ubiquitin DNA sequences were isolated from the higher plant Arabidopsis thaliana L. by screening a lambda-gt11 genomic library with antibodies raised against oat and human ubiquitin. DNA sequence analysis showed that the predicted protein sequence is 100% conserved with that found in oat and barley and differs by only three residues to that found in animals. This gene (UBQ4) encodes a ubiquitin polyprotein with five repeats contiguously linked with no intervening sequences in the coding region and a C-terminal extension of Ser-Phe. Genomic Southern blot analysis showed that ubiquitin sequences comprise a multigene family of approximately 11 members in Arabidopsis. Northern blot analysis identified at least four transcript size classes, which accumulate in sizes ranging from 800 to 1900 bases. A 5'-specific probe for the UBQ4 gene was used to show that after 2 h heat shock stress, the steady state mRNA level decreased significantly in flowers/buds but not in leaves. The UBQ4 transcript accumulates in a differential manner, accumulating to higher levels in germinating tissue, etiolated tissue, and flowers/buds than in mature leaves, roots, or stems.

Tobacco mosaic virus particles contain ubiquitinated coat protein subunits

Virions of tobacco mosaic virus (TMV) are composed of a single strand of RNA, encapsidated in about 2130 copies of a coat protein of MW 17,500. Asselin and Zaitlin [Virology 91, 173-181 (1978)] demonstrated that virion preparations also contained small amounts of a second protein of MW 26,500, which they termed "H protein." H protein, detectable to an average frequency of one per virion, was thought to be a protein of host origin. Subsequent studies [Collmer, Vogt, and Zaitlin, Virology 126, 429-448 (1983)] showed the H protein was comprised of a backbone of TMV coat protein, linked by a postulated isopeptide bond to a small protein that probably was of host origin. The host-derived moiety of H protein is shown here to be ubiquitin, most probably coupled to the coat protein at lysine 53. This finding is based on microsequencing of the H protein, and is substantiated by immunoblotting analysis with antibodies to human ubiquitin. Conjugated ubiquitin was detected in virions of all five strains of the virus tested. To our knowledge, this is the first report of a ubiquitinated viral structural protein.

The gene coding a ubiquitin-activating enzyme may locate on X chromosome

tsBN75 cells which have a ts defect in the S phase have a mutation linked to the gene of hypoxanthine phosphoribosyl transferase and cannot complement ts85 cells which have a ts defect in the ubiquitin-activating enzyme. The ubiquitin-activating enzyme may be required for completion of the S phase.

Influence of neuronal location on antigenic properties of neurofibrillary tangles

We quantitatively assessed the antigenic properties of the neurofibrillary tangles (NFT) located in neurons of the tegmental nuclei of the pontine raphe in progressive supranuclear palsy (PSP) and Alzheimer's disease (AD). These properties were then compared with those of NFT of AD located in hippocampal neurons. Antibodies known to react with cortical NFT of AD were used to stain sections from PSP, AD, and control cases. The reaction with the straight filaments of NFT of PSP and with the paired helical filaments of pontine NFT of AD was ascertained by immunoelectron microscopy. The results show that, despite the ultrastructural difference, straight filaments in NFT of PSP and paired helical filaments in NFT of AD share antigenic properties when they are located in the same neuronal population. In contrast, paired helical filaments located in the cerebral cortex are antigenically different from those in pontine nuclei. Location, more than structure, may play a role as determinant of antigenic properties in straight filaments of PSP and paired helical filaments of AD.

Microinjected ribonuclease A as a probe for lysosomal pathways of intracellular protein degradation

There are multiple pathways of intracellular protein degradation, and molecular determinants within proteins appear to target them for particular pathways of breakdown. We use red cell-mediated microinjection to introduce radiolabeled proteins into cultured human fibroblasts in order to follow their catabolism. A well-characterized protein, bovine pancreatic ribonuclease A (RNase A), is localized initially in the cytosol of cells after microinjection, but it is subsequently taken up and degraded by lysosomes. This lysosomal pathway of proteolysis is subject to regulation in that RNase A is taken up and degraded by lysosomes at twice the rate when serum is omitted from the culture medium. Subtilisin cleaves RNase A between residues 20 and 21, and the separated fragments are termed RNase S-peptide (residues 1-20) and RNase S-protein (residues 21-124). Microinjected RNase S-protein is degraded in a serum-independent manner, while RNase S-peptide microinjected alone shows a twofold increase in degradation in response to serum withdrawal. Furthermore, covalent linkage of S-peptide to other proteins prior to microinjection causes degradation of the conjugate to become serum responsive. These results show that recognition of RNase A and certain other proteins for enhanced lysosomal degradation during serum withdrawal is based on some feature of the amino-terminal 20 amino acids. The entire S-peptide is not required for enhanced lysosomal degradation during serum withdrawal because degradation of certain fragments is also responsive to serum. We have identified the essential region to be within residues 7-11 of RNase S-peptide (Lys-Phe-Glu-Arg-Gln; KFERQ). To determine whether related peptides exist in cellular proteins, we raised antibodies to the pentapeptide. Affinity-purified antibodies to KFERQ specifically precipitate 25-35% of cellular proteins, and these proteins are preferentially degraded in response to serum withdrawal. Computer analyses of known protein sequences indicate that proteins degraded by lysosomes at an enhanced rate in response to serum withdrawal contain peptide regions related, but not identical, to KFERQ. We suggest two possible peptide motifs related to KFERQ and speculate about possible mechanisms of selective delivery of proteins to lysosomes based on such peptide regions.

Complete cDNA sequence of a Dictyostelium ubiquitin with a carboxy-terminal tail and identification of the protein using an anti-peptide antibody

The complete sequence of a Dictyostelium discoideum cDNA is presented that codes for monoubiquitin extended at its C-terminus by a 52 amino acid tail. The sequence of both the ubiquitin portion and the tail is highly homologous to the one of Saccharomyces cerevisiae and to a partial mouse sequence. The highly basic tail sequence contains a putative metal and nucleic acid-binding motif. The gene encoding the 0.6 kb mRNA of the C-terminally extended ubiquitin is represented only once in the haploid genome. The 0.6 kb mRNA as well as its translation product, a 15 kDa protein, is expressed in exponentially growing cells and remains present for at least 5 h of development. Using antibodies against a synthetic peptide that corresponds to the C-terminal amino acid sequence, a 15 kDa protein containing the extension a synthetic peptide that corresponds to the C-terminal amino acid sequence, a 15 kDa protein containing the extension was also detected in yeast.

Defect in the development of thermotolerance in the mouse temperature-sensitive mutant ts85 lacking ubiquitin-activating enzyme

We investigated the effect of heat shock on the development of thermotolerance using mouse FM3A cells and the temperature-sensitive mutant ts85. The shift-up incubation of FM3A from 33 to 39.5 degrees induced thermotolerance to subsequent heating at 44 degrees. In contrast, the similar treatment of ts85 at the nonpermissive temperature of 39.5 degrees could not induce thermotolerance. Furthermore, when ts85 cells were treated at 33 degrees after being heated at 44 degrees, they developed a reduced level of thermotolerance as compared with that developed in FM3A cells. Since ts85 cells are defective in ubiquitin-activating enzyme, these results suggest a role of the ubiquitin-protein conjugation system in the development of thermotolerance.

Searching for the function of tissue transglutaminase: its possible involvement in the biochemical pathway of programmed cell death

Although several details are still missing, the biological role of two of the three well characterized transglutaminases in mammals, namely blood coagulation factor XIII and keratinocyte transglutaminase, is established. The function of the third one called the tissue type is still an enigma. Its constant localization in endothelial and smooth muscle cells of all organs, in heart muscle, in medullary interstitial and mesangial cells of kidney, and its induction in a number of other cell types under a variety of conditions suggest multiple functions. According to our results its participation in the biochemical pathway leading to programmed cell death (apoptosis), a basic cellular phenomenon of physiological significance, may be one of these functions.

Enzymes of nucleotide metabolism: the significance of subunit size and polymer size for biological function and regulatory properties

The 72 enzymes in nucleotide metabolism, from all sources, have a distribution of subunit sizes similar to those from other surveys: an average subunit Mr of 47,900, and a median size of 33,300. The same enzyme, from whatever source, usually has the same subunit size (there are exceptions); enzymes having a similar activity (e.g., kinases, deaminases) usually have a similar subunit size. Most simple enzymes in all EC classes (except class 6, ligases/synthetases) have subunit sizes of less than 30,000. Since structural domains defined in proteins tend to be in the Mr range of 5,000 to 30,000, it may be that most simple enzymes are formed as single domains. Multifunctional proteins and ligases have subunits generally much larger than Mr 40,000. Analyses of several well-characterized ligases suggest that they also have two or more distinct catalytic sites, and that ligases therefore are also multifunctional proteins, containing two or more domains. Cooperative kinetics and evidence for allosteric regulation are much more frequently associated with larger enzymes: such complex functions are associated with only 19% of enzymes having a subunit Mr less than or equal to 29,000, and with 86% of all enzymes having a subunit Mr greater than 50,000. In general, larger enzymes have more functions. Only 20% of these enzymes appear to be monomers; the rest are homopolymers and rarely are they heteropolymers. Evidence for the reversible dissociation of homopolymers has been found for 15% of the enzymes. Such changes in quaternary structure are usually mediated by appropriate physiological effectors, and this may serve as a mechanism for their regulation between active and less active forms. There is considerable structural organization of the various pathways: 19 enzymes are found in various multifunctional proteins, and 13 enzymes are found in different types of multienzyme complexes.

Regulation of skeletal muscle myofibrillar protein degradation: relationships to fatigue and exercise

1. Exercise results in large alterations in cellular metabolic homeostasis and protein turnovers. Exhaustive exercise (as well as starvation, dystrophy, motor nerve disease) results in myofibrillar degradation and has been associated with the decreased force generating capabilities of muscle at fatigue. 2. Complete protein degradation is accomplished by the combined actions of non-lysosomal and lysosomal proteases and the initial breakdown of myofibrillar protein appears to be non-lysosomal mediated. 3. Current evidence suggests that covalent modification (mixed-function oxidation, formation of mixed disulfides, oxidation of methionine residues and phosphorylation) of proteins may mark them for degradation by rendering them more susceptible to proteolytic attack. 4. The rate of covalent modification can be controlled by the level of stabilizing and destabilizing ligands and by factors affecting the activity of the marking reaction. 5. The activities of individual proteases may be controlled by activators and inhibitors. 6. It is suggested that the large alterations in metabolism (hormonal profiles, energy status, redox status and Ca2+ levels) which accompany exercise serve to activate specific proteases and/or induce covalent modifications which mark specific myofibrillar proteins for subsequent proteolytic attack.

Cloning and sequence analysis of a cDNA encoding poly-ubiquitin in human ovarian granulosa cells

A cDNA clone, pHGR21 encoding poly-ubiquitin, was isolated from a human ovarian granulosa cDNA library. This clone contained three complete, and part of a fourth, ubiquitin coding sequence joined head to tail with no spacer sequences. Northern analysis employing a restriction fragment comprising a complete ubiquitin coding unit indicated the existence of two mRNA species of 1.1kb and 2.8kb. Sequence comparison of pHGR21 with the known two human ubiquitin genes revealed differences to the human ubiquitin-3 repeat gene but significant homology to the human ubiquitin-9 repeat gene. The untranslated 3'-region and the adjacent ubiquitin coding repeat were found to be identical to that of the human ubiquitin-9 repeat gene. The other 3 ubiquitin coding repeats were of close homology to the fourth ubiquitin coding repeat of the human ubiquitin-9 repeat gene. These findings suggest the existence of yet another human poly-ubiquitin gene.

The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme

The RAD6 gene of the yeast Saccharomyces cerevisiae is required for a variety of cellular functions including DNA repair. The discovery that the RAD6 gene product can catalyse the covalent attachment of ubiquitin to other proteins suggests that the multiple functions of the RAD6 protein are mediated by its ubiquitin-conjugating activity.

Intracellular localisation of phytochrome and ubiquitin in red-light-irradiated oat coleoptiles by electron microscopy

The intracellular localisation of phytochrome and ubiquitin in irradiated oat coleoptiles was analysed by electron microscopy. We applied indirect immunolabeling with polyclonal antibodies against phytochrome from etiolated oat seedlings or polyclonal antibodies against ubiquitin from rabbit reticulocytes, together with a goldcoupled second antibody, on serial ultrathin sections of resin-embedded material. Immediately after a 5-min pulse of red light-converting phytochrome from the red-absorbing (Pr) to the far-redabsorbing (Pfr) form-the label for phytochrome was found to be sequestered in electron-dense areas. For up to 2 h after irradiation, the size of these areas increased with increasing dark periods. The ubiquitin label was found in the same electrondense areas only after a dark period of 30 min. A 5 min pulse of far-red light, which reverts Pfr to Pr, given immediately after the red light did not cause the electron-dense structures to disappear; moreover, they contained the phytochrome label immediately after the far-red pulse. In contrast, after the reverting far-red light pulse, ubiquitin could only be visualised in the electron-dense areas after prolonged dark periods (i.e. 60 min). The relevance of these data to light-induced phytochrome pelletability and to the destruction of both Pr and Pfr is discussed.

Induction of sequence-specific binding of Drosophila heat shock activator protein without protein synthesis

Drosophila tissue culture cells stimulated by heat shock contain high levels of heat shock activator protein, which binds specifically to the heat-shock control DNA element. In contrast, nonshocked cells have low basal levels of binding activity. Here, we show that within 30 seconds of heat shock of intact cells the sequence-specific binding activity in whole cell extracts increases significantly, reaching a plateau by 5 min after the start of the shock; removal of the heat stimulus returns the activity to basal levels. Known chemical inducers of heat-shock genes elicit a similar pattern of specific binding activity. Moreover, this pattern is observed in the presence of protein synthesis inhibitors, even if the stimulus-withdrawal is repeated sequentially through five cycles. Our results are inconsistent with models which propose proteolysis as the chief means of mediating heat-shock transcriptional control. Rather, they suggest that heat shock activator pre-exists in normal cells in a nonbinding form, which is converted upon cell stimulus to a high affinity, sequence-specific binding form, most probably by a post-translational modification. This conversion may be crucial for the transcriptional activation of heat shock genes.

Ubiquitin genes as a paradigm of concerted evolution of tandem repeats

Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken, Xenopus, Drosophila, barley, and yeast have recently been determined. By analysis of these data we show that ubiquitin is evolving more slowly than any other known protein, and that this (together with its gene organization) contributes to an ideal situation for the occurrence of concerted evolution of tandem repeats. By contrast, there is little evidence of between-cluster concerted evolution. We deduce that in ubiquitin genes, concerted evolution involves both unequal crossover and gene conversion, and that the average time since two repeated units within the polyubiquitin locus most recently shared a common ancestor is approximately 38 million years (Myr) in mammals, but perhaps only 11 Myr in Drosophila. The extreme conservatism of ubiquitin evolution also allows the inference that certain synonymous serine codons differing at the first two positions were probably mutated at single steps.

The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses

Conjugation of ubiquitin to intracellular proteins mediates their selective degradation in eukaryotes. In the yeast Saccharomyces cerevisiae, four distinct ubiquitin-coding loci have been described. UBI1, UBI2, and UBI3 each encode hybrid proteins in which ubiquitin is fused to unrelated sequences. The fourth gene, UBI4, contains five ubiquitin-coding elements in a head-to-tail arrangement, and thus encodes a polyubiquitin precursor protein. A precise, oligonucleotide-directed deletion of UBI4 was constructed in vitro and substituted in the yeast genome in place of the wild-type allele. ubi4 deletion mutants are viable as vegetative cells, grow at wild-type rates, and contain wild-type levels of free ubiquitin under exponential growth conditions. However, although ubi4/UBI4 diploids can form four initially viable spores, the two ubi4 spores within the ascus lose viability extremely rapidly, apparently a novel phenotype in yeast. Furthermore, ubi4/ubi4 diploids are sporulation-defective. ubi4 mutants are also hypersensitive to high temperatures, starvation, and amino acid analogs. These three conditions, while diverse in nature, are all known to induce stress proteins. Expression of the UBI4 gene is similarly induced by either heat stress or starvation. These results indicate that UBI4 is specifically required for the resistance of cells to stress, and that ubiquitin is an essential component of the stress response system.

Proteinase yscD mutants of yeast. Isolation and characterization

Mutants of the yeast Saccharomyces cerevisiae, devoid of proteinase yscD activity, were isolated by screening for the inability of mutagenized cells to hydrolyze Ac-Ala-Ala-Pro-Ala-beta-naphthylamide in situ. One of the selected mutants bears a thermolabile activity pointing to the gene called PRD1 as being the structural gene for proteinase yscD. All mutants isolated fell into one complementation group. The defect segregates 2:2 in meiotic tetrads indicating a single gene mutation, which was shown to be recessive. Diploids heterozygous for PRD1 display gene dosage. The absence of proteinase yscD did not affect mitotic growth under rich or poor growth conditions, neither mating nor ascopore formation. Also growth of mutant cells after a nutritional shift-down was not altered. Inactivation of enzymes tested which are subject to carbon-catabolite inactivation, a process proposed to be of proteolytic nature, is not affected by the absence of proteinase yscD. Protein degradation rates in growing cells, in cells under conditions of differentiation or heat shock, showed no obvious alteration in the absence of proteinase yscD activity. Also inactivation of alpha-factor pheromone was not affected by proteinase yscD absence. Normal growth of mutant cells on glycerol indicates that the enzyme is not involved in any vital event in mitochondrial biogenesis.

The glucocorticoid receptor protein binds to transfer RNA

The glucocorticoid receptor from mouse AtT-20 cells exists in three forms: the untransformed receptor (9.1S; Mr of 319,000), a large oligomeric molecule that does not bind to DNA; the transformed receptor (4S; Mr of 96,000), which is formed by dissociation of untransformed receptor after steroid binding and which binds to DNA to modulate gene expression; and an intermediate size receptor (6S; Mr of 132,000), which also binds to DNA and contains a bound small RNA molecule. This RNA species has now been purified and identified as transfer RNA (tRNA). The three tRNA's for the basic amino acids accounted for about 78% of the total amino acid-accepting activity [arginine (52%), lysine (17%), and histidine (9%)], while the remaining 22% was represented by six other tRNA species. This tRNA-binding activity of the glucocorticoid receptor may reflect post-transcriptional mechanisms of regulating gene expression, such as alterations in the translational efficiency of or the modulation of the stability of hormone-induced proteins.

Simplified methods for isolation of ubiquitin from erythrocytes. Generation of ubiquitin polymers

1. Ubiquitin has been isolated from bovine erythrocytes by procedures in which the hemoglobin was removed by denaturation with either ethanol-chloroform mixtures or by heating. 2. The proteins soluble to the denaturation step were removed by 3% sodium trichloroacetate (TCA) at pH 2.0-2.5 or by 5% TCA. 3. Ubiquitin was isolated in relatively high yield from the TCA insoluble fraction by use of single ion-exchange chromatographic and gel permeation steps. 4. Ubiquitin shows relatively little cross-linking upon treatment with glutaraldehyde or with dimethyl suberimidate. Heating of the glutaraldehyde treated material in 4 M guanidine, however, leads to marked aggregation. 5. The polymers of ubiquitin react strongly with antibody in an immunoblot assay.

In vivo half-life of a protein is a function of its amino-terminal residue

When a chimeric gene encoding a ubiquitin-beta-galactosidase fusion protein is expressed in the yeast Saccharomyces cerevisiae, ubiquitin is cleaved off the nascent fusion protein, yielding a deubiquitinated beta-galactosidase (beta gal). With one exception, this cleavage takes place regardless of the nature of the amino acid residue of beta gal at the ubiquitin-beta gal junction, thereby making it possible to expose different residues at the amino-termini of the otherwise identical beta gal proteins. The beta gal proteins thus designed have strikingly different half-lives in vivo, from more than 20 hours to less than 3 minutes, depending on the nature of the amino acid at the amino-terminus of beta gal. The set of individual amino acids can thus be ordered with respect to the half-lives that they confer on beta gal when present at its amino-terminus (the "N-end rule"). The currently known amino-terminal residues in long-lived, noncompartmentalized intracellular proteins from both prokaryotes and eukaryotes belong exclusively to the stabilizing class as predicted by the N-end rule. The function of the previously described posttranslational addition of single amino acids to protein amino-termini may also be accounted for by the N-end rule. Thus the recognition of an amino-terminal residue in a protein may mediate both the metabolic stability of the protein and the potential for regulation of its stability.

Enhancement of immunoblot sensitivity by heating of hydrated filters

Immunoblots of either dot or Western type were exposed to heat before reaction with antibody. Dramatic increases in immunoblot sensitivity were seen for certain antigen-antibody pairs after heating of either dry or hydrated nitrocellulose filters at or above 100 degrees C. Heating of filters in the hydrated state improved the linearity of immunodetection and produced the highest signal-to-noise ratio. This treatment greatly increased immunoblot sensitivity with several peptide-generated antibodies, whereas decreased sensitivity was seen with antibodies against native proteins. Heating of hydrated filters after antigen immobilization is thus a potentially powerful way to increase the sensitivity of immunoblot analysis for antibodies that preferentially recognize epitopes in denatured proteins.