Purification and initial characterization of ubiquitin from the higher plant, Avena sativa

DNA damage-induced ubiquitylation of proteasome controls its proteolytic activity

Stability of proteins is largely controlled by post-translational covalent modifications. Among those, ubiquitylation plays a central role as it marks the proteins for proteasome-dependent degradation. Proteolytic activities of proteasomes are critical for execution of various cellular processes, including DNA damage signaling and repair. However, very little is known about the regulation of proteasomal activity in cells during genotoxic stress. Here we investigated post-translational modifications of the 20S proteasomal subunits upon DNA damage induced by doxorubicin. Using mass-spectrometry, we found novel sites of phosphorylation and ubiquitylation in multiple proteasome subunits upon doxorubicin treatment. Ectopic co-expression of proteasome subunits and tagged ubiquitin confirmed the presence of ubiquitylated forms of PSMA5, PSMA1, PSMA3 and PSMB5 in cells. Moreover, we demonstrated that ubiquitylation in vitro inhibited chymotrypsin-like and caspase-like activities of proteasomes. In vivo, doxorubicin increased the activity of proteasomes, paralleling with attenuation of the overall level of proteasome ubiquitylation. Collectively, our results suggest a novel mechanism whereby the proteolytic activities of proteasomes are dynamically regulated by ubiquitylation upon DNA damage.

Histidine-tagged ubiquitin substitutes for wild-type ubiquitin in Saccharomyces cerevisiae and facilitates isolation and identification of in vivo substrates of the ubiquitin pathway

A general method for purification of any substrate of the ubiquitin pathway, the major eukaryotic proteolytic pathway, should utilize the common characteristic of covalent linkage of ubiquitin to substrate lysyl residues. The utility of a N-terminal histidine-tagged ubiquitin (HisUb) for in vivo conjugation and isolation of ubiquitinated proteins by metal chelation chromatography is conditioned by the requirement that HisUb conjugate to the same set of proteins as wild-type ubiquitin. Stringent in vivo tests with Saccharomyces cerevisiae strains expressing ubiquitins only from plasmids were performed to show that HisUb could substitute for wild-type ubiquitin. The utility of HisUb as a method for purification of proteins ubiquitinated in vivo was demonstrated by metal chelation chromatography of yeast extracts expressing HisUb and immunoblotting for Rpb1, the largest subunit of RNA polymerase II. A fraction of Rpb1 was present in the ubiquitinated form in vivo. The ability to use HisUb expression in transgenic organisms that retain expression of their endogenous ubiquitin genes was demonstrated through transgenic Arabidopsis thaliana expressing HisUb or its variant HisUbK48R. UbK48R is a version of ubiquitin capable of conjugation to proteins, but cannot serve as an attachment site for ubiquitin via the major in vivo interubiquitin linkage. Whereas transgenic plants expressing HisUb showed insignificant enrichment of ubiquitinated proteins, transgenic Arabidopsis lines expressing HisUbK48R gave a much better yield.

A new member of the leucyl aminopeptidase family purified and identified from a marine unicellular algae

Leucyl aminopeptidase (LAP; EC 3.4.11.1) activity was purified from crude extracts of the marine unicellular algae Gonyaulax polyedra by a combination of hydrophobic interaction with phenyl sepharose, DEAE-cellulose, and mono-Q HR5/5 ion-exchange chromatography. The undenaturated protein has a molecular mass of about 110 kD and based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the enzyme appears to be composed of two possibly identical subunits of 55 kD. The identity of the protein was confirmed by a cross-reaction of the purified protein with an antibody raised against a commercial LAP. Biochemical characterization showed that the Gonyaulax enzyme was similar to most of the previously described LAPs. Gonyaulax LAP is a metallo-enzyme since EDTA and 1,10-phenathroline significantly inhibited activity. Addition of the metal ions Zn(2+), Cu(2+) inhibited 80% of LAP activity, suggesting they are not the natural cofactors of the enzyme. Other metals, such as Ca(2+), Co(2+), Mn(2+), or Mg(2+) (concentrations up to 4 mM), caused no alteration in the total activity of Gonyaulax LAP.

Proteolysis in plants: mechanisms and functions

Proteolysis is essential for many aspects of plant physiology and development. It is responsible for cellular housekeeping and the stress response by removing abnormal/misfolded proteins, for supplying amino acids needed to make new proteins, for assisting in the maturation of zymogens and peptide hormones by limited cleavages, for controlling metabolism, homeosis, and development by reducing the abundance of key enzymes and regulatory proteins, and for the programmed cell death of specific plant organs or cells. It also has potential biotechnological ramifications in attempts to improve crop plants by modifying protein levels. Accumulating evidence indicates that protein degradation in plants is a complex process involving a multitude of proteolytic pathways with each cellular compartment likely to have one or more. Many of these have homologous pathways in bacteria and animals. Examples include the chloroplast ClpAP protease, vacuolar cathepsins, the KEX2-like proteases of the secretory system, and the ubiquitin/26S proteasome system in the nucleus and cytoplasm. The ubiquitin-dependent pathway requires that proteins targeted for degradation become conjugated with chains of multiple ubiquitins; these chains then serve as recognition signals for selective degradation by the 26S proteasome, a 1.5 MDa multisubunit protease complex. The ubiquitin pathway is particularly important for developmental regulation by selectively removing various cell-cycle effectors, transcription factors, and cell receptors such as phytochrome A. From insights into this and other proteolytic pathways, the use of phosphorylation/dephosphorylation and/or the addition of amino acid tags to selectively mark proteins for degradation have become recurring themes.

Functional characterization of the ubiquitin variant encoded by the baculovirus Autographa californica

The marked evolutionary conservation of ubiquitin is assumed to arise from constraints imposed by folding, stability, and interaction of the polypeptide with various components of the ATP, ubiquitin-dependent degradative pathway. The present studies characterize the most divergent (75% identity) of the species-specific ubiquitin isoforms encoded as a late gene product of the baculovirus Autographa californica [Guarino, L. A. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 409-413]. Viral ubiquitin supports 40% of the rate of ATP-dependent degradation exhibited by eukaryotic ubiquitin. Inhibition of proteolysis correlated with a lower steady-state concentration of ubiquitin-conjugated degradative intermediates. Rate studies revealed that viral ubiquitin exerts its effect at the step of isopeptide ligase-catalyzed (E3) ubiquitin conjugation since viral and eukaryotic polypeptides are identical in their abilities to support ATP-coupled activation by E1 and transthiolation to E2 carrier proteins. Other studies demonstrated viral ubiquitin severely attenuated the rate of K48-linked multiubiquitin chain formation in E3-independent conjugation catalyzed by recombination yeast CDC34 or rabbit reticulocyte E232K but not chain elongation of alternate linkages formed by yeast RAD6 or human E2EPF. The latter observations suggest nonconserved positions on viral ubiquitin constitute recognition signals for K48-linked chain formation. Sequence comparison of species-specific ubiquitin isoforms indicates that nonconserved positions localized to a defined region on the polypeptide surface distinct from the basic face required for E1 binding. These results suggest this novel ubiquitin isoform may function in baculoviral replication to block destruction of a short-lived protein(s) by the host degradative pathway, targeted through either E2-catalyzed K48-linked multibiquitin chain formation or general E3-mediated conjugation.

Ubiquitin in the prokaryote Anabaena variabilis

The ubiquitin-dependent pathway for protein degradation has been found to play a major role in controlling protein turnover in the cell. Ubiquitin is one of the most conserved proteins yet identified, and up until now it has been thought to be present only in eukaryotes and archaebacteria. This is the first report on the detection and purification of ubiquitin from a eubacterium, the cyanobacterium Anabaena variabilis. The purification procedure included a heat denaturing step, fractionated ammonium sulfate precipitation, two gel filtration runs (Sephadex G-50 and Superose 12), and a final hydroxylapatite chromatography. Comparisons with bovine ubiquitin showed a high similarity with respect to antigenicity to anti-ubiquitin (bovine), molecular mass (M(r) = 6,000), isoelectric point (pI 6.5), and NH2-terminal sequence. The existence of ubiquitin in A. variabilis was confirmed by Southern hybridization. In in vitro experiments both cyanobacterial and bovine ubiquitin were covalently attached to several target proteins from A. variabilis, respectively. Data are presented which suggest ubiquitination of dinitrogenase reductase, the Fe-protein subunit of nitrogenase. Our findings imply that ubiquitination equivalent to the eukaryotic system is instrumental in this organism.

Ubiquitin in a lower plant. Characterization of ubiquitin-encoding DNA and RNA from Chlamydomonas reinhardii

A detailed characterization of Chlamydomonas reinhardii cDNAs encoding ubiquitin 52-amino-acid fusion proteins is presented in this study. While two cDNAs (designated UBI1 and UBI3) encode the complete ubiquitin extension protein, the third one (UBI2) lacks a minor part of the 5' region as well as a poly(A) tail. Differences between UBI1 and UBI3 are observed in the length of the poly(A) domain (13 versus 46 adenines) and in the lack of three nucleotides at the 3' noncoding region of UBI3. According to Northern blot experiments using UBI1 as a homologous probe, at least six members of the C. reinhardii ubiquitin gene family are transcriptionally active at regular conditions. During application of severe stress (heat shock in light and darkness, and photoinhibition), the transcription of the UBI1 mRNA substantially decreases. This effect is most drastically induced by application of heat shock to illuminated cells.

Isolation and quantitation of ubiquitin from rat brain

A fast and sensitive method for the isolation and quantitation of cytoplasmic ubiquitin from brain by reversed-phase high-performance liquid chromatography is described. Cytosol from brain tissue was obtained by differential centrifugation and, after perchloric acid treatment, the sample was concentrated and ubiquitin was quantitatively isolated by means of a single chromatographic run. The amino acid composition, molecular weight, and primary structure of the pure protein were identified. The addition of monoiodinated 125I-ubiquitin to the sample as an internal standard indicated high native ubiquitin recovery. Statistical analysis carried out on different preparations and standardization of the chromatographic system indicated both the accuracy and the reproducibility of the method.

Proteolytic activity during senescence of plants

Although information has rapidly developed concerning the intracellular localization of plant proteins, relatively few reports concern the intracellular location of endo- and exo-proteolytic activities. Relatively few proteases have been purified, characterized, and associated with a specific cellular location. With the exception of the processing proteases involved in transport of proteins across membranes, little progress has yet been made concerning determination of in vivo products of specific proteases. Information on the turnover of individual proteins and the assessment of rate-limiting steps in pathways as proteins are turned over is steadily appearing. Since chloroplasts are the major site of both protein synthesis and, during senescence, degradation, it was important to show unambiguously that chloroplasts can degrade their own constituents. Another important contribution was to obtain evidence that the chloroplasts contain proteases capable of degrading their constituents. This work has been more tenuous because of the low activities found and the possibility of contamination by vacuolar enzymes during the isolation of organelles. The possible targeting of cytoplasmic proteins for degradation by facilitating their transport into vacuoles is a field which hopefully will develop more rapidly in the future. Information on targeting of proteins for degradation via the ubiquitin (Ub) degradation pathway is developing rapidly. Future research must determine how much unity exists across the different eukaryotic systems. At present, it has important implications for protein turnover in plants, since apparently Ub is involved in the degradation of phytochrome. Little information has been developed regarding what triggers increased proteolysis with the onset of senescence, although it appears to involve protein synthesis. Thus far, the evidence indicates that the complement of proteases prior to senescence is sufficient to carry out the observed protein degradation. This field of study has great practical implications, e.g. maintaining photosynthesis during seed-fill in order to obtain greater crop yields. The current use of stay green' variants in the populations of several crop plants to produce increased yields shows the potential for future development. The near future should see exciting discoveries in these areas of research that will have far reaching effects on the construction of transgenic plants for future research accomplishments and agricultural use.

Aging and cellular maturation cause changes in ubiquitin-eye lens protein conjugates

The eye lens is a useful tissue for studying phenomena related to aging since it can be separated into differentially aged or matured zones. This work establishes correlations between ubiquitin-lens protein conjugating capabilities and age, as well as the stage of maturation of bovine lens tissue. When exogenous 125I-ubiquitin was combined with supernatants of epithelial (least mature), cortex, and core (most mature) tissue, ATP-dependent conjugation of 125I-ubiquitin to lens proteins was most effective with the epithelial tissue preparation. Conjugate formation was greatest when lenses were obtained from young animals. Supernatants from cultured bovine lens epithelial (BLE) cells conjugated more 125I-ubiquitin to lens proteins than any tissue preparation. In all cases the predominant conjugates formed in these cell-free assays were of high molecular mass, although conjugates with masses in the 25-70 kDa range were also observed. Lens tissue and cultured BLE cell preparations were also probed with antibodies to ubiquitin to detect in vivo ubiquitin-lens protein conjugates. There was more free ubiquitin and ubiquitin conjugates in tissue from young as compared with older lenses. The greatest levels of conjugates were observed in cultured BLE cells. Specificity in the ubiquitination system is indicated since some of the conjugates formed in vivo appear identical to those formed in the cell-free assays and in reticulocytes using exogenous 125I-ubiquitin. Upon development and maturation of lens tissue (i.e., core as opposed to epithelium), there is accumulation of lower molecular mass conjugates.

Sequence analysis and transcriptional regulation by heat shock of polyubiquitin transcripts from maize

We have isolated a maize ubiquitin cDNA clone which encodes one partial and three full-length, identical 76 amino acid repeats, in a polyprotein conformation. The deduced amino acid sequence of the mature monomeric polypeptide is identical to that determined for three other plants, barley, oat, and Arabidopsis, and differs from yeast and animal ubiquitin by only two and three amino acids, respectively. Hybridization of the cDNA clone to restriction endonuclease-digested genomic DNA revealed that ubiquitin is encoded by a small multigene family in maize. Northern blot analysis of poly(A)(+) RNA indicated that multiple ubiquitin mRNAs of 2.1, 1.6 and 0.8 kb are produced in maize shoots and roots. The abundance of the largest (2.1 kb) of these transcripts increased transiently 3- to 4-fold over the first 1 to 3 h in seedlings that were subjected to heat shock, and then returned dramatically within 1 h almost to the preshocked level. In contrast, the two smaller transcripts showed little or no change following heat shock. Run-on transcription assays in isolated maize nuclei showed a heat shock-induced increase in ubiquitin run-on transcripts that paralleled the increase in mature 2.1 kb mRNA levels over the first 3 h following the heat shock treatment. This result indicates that heat shock regulates ubiquitin gene expression at least in part at the transcriptional level. The subsequent rapid decline in steady-state mRNA levels, on the other hand, was not preceded by decreased ubiquitin gene transcription, raising the possibility of both transcriptional and posttranscriptional regulation. The run-on transcription assays also revealed a transient 5-fold reduction in rRNA gene transcription following heat shock, indicating that the transcriptional machinery for these genes is selectively sensitive to this stress.

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.

Isolation and characterization of ATP-dependent proteolytically active ubiquitin in cock testis

1. We have successfully isolated and purified ubiquitin from cock testis by using an inhibitor, p-CMB (p-chloromercuribenzoate), which is one of the inhibitors specific for thiol-proteases and with the following procedures: heating up to 85 degrees C, ammonium sulfate fractionation, gel filtration on Sephadex G-75, chromatography on DE-52 and CM-11 and lyophilization. 2. Amino-acid analysis showed that Ub isolated from cock testis has 76 residues including 6 glycines. 3. Hydrazinolysis and carboxypeptidase digestion were also performed: the C-terminal residue is glycine. 4. The purity was checked by analytical SDS-PAGE and the isolated Ub exhibited only one band. 5. The Ub-dependent proteolysis experiment showed that this Ub was ATP-dependently proteolytically active. 6. In this paper we present evidence that a thiol enzyme is present during the purification procedure.

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.

Proteases of Melilotus alba mesophyll protoplasts : II. General properties and effectiveness in degradation of cytosolic and vacuolar enzymes

Proteases from mesophyll protoplasts of Melilotus alba were identified by standard proteolytic assays and separated using different chromatographic techniques. Their characterization also included their subcellular location. Besides the evidence for the multiplicity of the proteolytic enzymes, two protease sets were distinguished endopeptidases, which are exclusively vacuolar, and aminopeptidases, which are widely distributed throughout the cell. Cytosol-located enzymes were tested as substrates of the two sets of proteases, by studying comparatively the time-course changes of enzyme activities during incubation in total protoplast extracts, or in cytosol fractions devoid of vacuolar proteases. The degradation of phosphoenolpyruvate-carboxylase protein, a typical cytosolic enzyme, in the presence of purified amino-and endopeptidases, was also estimated by immunoprecipitation studies. Only the vacuolar endopeptidases are effective in the degradation of cytosolic enzymes. Hydrolytic enzyme activities mostly of vacuolar origin were very stable during incubation in total protoplast extracts. These proteins therefore appear to be particularly resistant to proteolytic attack. The results indicate that, in plants, the effective proteolytic system acting on cytosolic enzymes seems to be vacuole-located, and that the selectivity in protein degradation may be imposed by the susceptibility of the protein being degraded and by its transfer into the vacuoles.

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.

Structure and activities of a variant ubiquitin sequence from bakers' yeast

Ubiquitin is an extremely conserved protein, with an identical sequence throughout the animal kingdom. However, the gene sequence of the yeast protein [Ozkaynak, E., Finley, D., & Varshavsky, A. (1984) Nature (London) 312, 663-666] predicts three amino acid differences. This implies that some functions or binding interactions of ubiquitin are different in yeast and animal cells. In an effort to define these differences, ubiquitin has been purified to homogeneity from bakers' yeast and characterized. Amino acid analysis of the protein and the isolated tryptic peptides confirms the primary structure of this protein as predicted from the gene sequence. This result indicates that the gene sequenced is the transcriptionally active gene from yeast. The conformation of yeast ubiquitin is similar to human ubiquitin as judged by circular dichroism, sensitivity to trypsin, and Stokes radius. Yeast and animal ubiquitins show identical activities in supporting ubiquitin-dependent protein degradation and in the ATP-pyrophosphate exchange reaction catalyzed by the purified ubiquitin-adenylating enzyme. Thus, the three conservative amino acid differences between yeast and animal ubiquitins have very little effect on the structure of ubiquitin or its activity in the ubiquitin-dependent proteolytic system. These results suggest that at least some of the evolutionary pressure preventing sequence variation among animal ubiquitins stems from one or more of its nonproteolytic functions.