Conjugation of [125I]ubiquitin to cellular proteins in permeabilized mammalian cells: comparison of mitotic and interphase cells.

[125I]Ubiquitin introduced into permeabilized hepatoma tissue culture (HTC) cells rapidly forms conjugates with endogenous proteins. A characteristic pattern of low mol. wt conjugates is obtained which includes the ubiquitinated histone, uH2A, and unknown molecular species with MrS of 14, 23, 26 (two bands) and 29 kd. A broad spectrum of higher mol. wt conjugates is also produced. The formation of all conjugates is absolutely dependent on ATP, and upon depletion of ATP they are rapidly broken down. The 14, 23 and 29 kd species are found in all subcellular fractions examined. uH2A is located exclusively in the nuclear fraction. The pair of 26 kd bands is specifically associated with the ribosome fraction. A considerable percentage of the higher mol. wt conjugates sediments with the small particle (100,000 g) fraction in the ultracentrifuge but is solubilized with deoxycholate, indicating that there are many membrane-associated conjugates. The pattern of ubiquitin conjugation in interphase and metaphase cells was compared. The incorporation of ubiquitin into uH2A was markedly reduced in metaphase cells whereas its incorporation into other low mol. wt conjugates and into high mol. wt conjugates was affected slightly, if at all. This shows that the known decrease of uH2A levels in metaphase is due to a specific effect on histone ubiquitination and not to a general decrease in ubiquitination activity or increase of isopeptidase activity. Changes in the levels of uH2A during mitosis measured by immunoblotting were similar to those estimated in permeabilized cells. These experiments indicate that permeabilized cells provide a useful approach to the study of rapidly turning over ubiquitin conjugates in mammalian cells.     

Changes in ubiquitin and ubiquitin-protein conjugates during seed formation and germination

Changes in both free ubiquitin and ubiquitin-protein conjugateswere followed in cotyledons of lupin (Lupinus albus L.) duringthe course of seed formation, from the flower to the dry seed,and during germination and seedling growth, from the dry seedto the senescing cotyledons. The observed levels of ubiquitinconjugates, detected by immunoblotting using antiubiquitin antibodiesand by autoradiography using ¹²⁵I-labelled ubiquitin, suggestan intense involvement of the ubiquitin-mediated proteolyticpathway during the highly regulated phases of seed formationand germination. High amounts of free ubiquitin are presentat all stages in all tissues examined. With the exception ofthe dry seed, the high molecular mass ubiquitin-protein conjugatesare also present at all stages. Higher amounts of these conjugateswere found during the initial stages of pod development andseed germination and during the most active phases of storageprotein deposition and degradation. Germination and seedlinggrowth in total darkness not only delays the degradation ofthe storage proteins, but also extends the period characterizedby the presence of a high amount of these conjugates. No suchconjugates were detected in the dry seeds, probably reflectingthe extremely low metabolic activity observed in these organs.A number of smaller molecular mass polypeptides were also detectedat different stages of seed development, germination and seedlinggrowth. Of particular interest is the abrupt accumulation ofan abundant 20 kDa polypeptide in the cotyledons during the4th day after imbibition, which is maintained in high amountsin these organs, rapidly declining after about 12–14 d.The pattern of accumulation of the 20 kDa polypeptide is controlledneither by light nor by the embryo axes, and large variationsin its concentration are observed during heat shock. Key words: Ubiquitin, ubiquitin-protein conjugates, seed storage proteins, protein synthesis, protein degradation     

Demonstration of ATP-Dependent, Ubiquitin-Conjugating Activities in Higher Plants

Ubiquitin is a highly conserved, 76-amino acid polypeptide with several important regulatory functions in both plants and animals that all arise from its covalent ligation to other cellular proteins. Here, we demonstrate that higher plants have the capacity to conjugate ubiquitin to other plant proteins in vitro. Using ¹²⁵I-labeled human ubiquitin as a substrate, conjugating activities were observed in crude etiolated tissue extracts from all species tested, including oats, rye, barley, corn, zucchini squash, pea, soybean, and sunflower. The reaction has a soluble distribution, is specific for ATP, and requires the protease inhibitor, leupeptin, to protect ubiquitin from inactivation during the assay. Conjugation is inhibited by N-ethylmaleimide and high concentrations of 2-mercaptoethanol suggesting that the mechanism of ubiquitin ligation in plants involves a similar thiolester intermediate to that found in the mammalian pathway. The conjugating activity in etiolated oat extracts is extremely labile with a half-life of about 20 minutes at 30°C. Detectable but low ATP-stimulated, conjugating activities were also observed in extracts from dry seeds and green leaves of oats. In addition to this conjugating activity, crude plant extracts have the capacity to degrade ubiquitin-protein conjugates formed in vitro. These results demonstrate that higher plants contain several of the enzymic activities necessary for ubiquitin's functions and provide a method for assaying ubiquitin conjugation in vitro.     

An ATP-synthesizing system in seeds

Using onion seed powder, a semi-in vitro system for ATP synthesis in seeds has been developed. The system requires AMP, phosphoenolpyruvate (PEP) and orthophosphate with apparent Km values of 0.8, 1.5 and 3.0 mM, respectively. ATP synthesis is pH-dependent with a sharp optimum at pH 6.4, it exhibits linearity with time up to 40 min, and with a seed powder concentration between 25 and 150 mg ml^-1. The system is stimulated by low concentrations (<25 mM) of K⁺ and Mg²⁺ but is inhibited by higher concentrations of K⁺ and Mg²⁺ as well as by low concentrations of Li⁺, Na⁺ and especially Ca²⁺. The maximal rate is about 5 pmol min^-1 mg seed powder^-1 in dry onion seeds. During seed imbibition the rate of activity increases by about 120% after 3 h, reaching a plateau which is steady up to 18 h, when the radicle emerges. A comparison of the ATP content in seeds during the early period of imbibition with the capacity of ATP synthesis at this stage reveals that the described system could provide, during germination, 100 times more ATP than that found in imbibed seeds. The system is shown to be present in ten different types of seeds.     

The degradative fate of ubiquitin-protein conjugates in nucleated and enucleated cells.

Covalent ligation of multiple copies of ubiquitin to proteins is known to target intracellular proteins for degradation by large molecular weight cytosolic proteinase(s). Ubiquitin protein conjugates are found in cytosolic cell compartments suggesting that ubiquitination may have multiple roles. We have detected ubiquitinated proteins in the lysosomal apparatus of normal fibroblasts and fibroblasts treated with lysosomal proteinase inhibitors. In contrast rabbit reticulocytes lack lysosomes. We present here direct evidence for ubiquitination of mitochondrial proteins during rabbit reticulocyte maturation. In addition ubiquitination appears to be associated with the terminal differentiation of human keratinocytes. These results suggest that: 1. ubiquitin-protein conjugates may be degraded lysosomally 2. organellar proteins may be degraded by the ubiquitin system 3. ubiquitination is involved in the programmed elimination of proteins and organelles from several cell types during differentiation.     

A proteomics approach to understanding protein ubiquitination

There is a growing need for techniques that can identify and characterize protein modifications on a large or global scale. We report here a proteomics approach to enrich, recover, and identify ubiquitin conjugates from Saccharomyces cerevisiae lysate. Ubiquitin conjugates from a strain expressing 6xHis-tagged ubiquitin were isolated, proteolyzed with trypsin and analyzed by multidimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for amino acid sequence determination. We identified 1,075 proteins from the sample. In addition, we detected 110 precise ubiquitination sites present in 72 ubiquitin-protein conjugates. Finally, ubiquitin itself was found to be modified at seven lysine residues providing evidence for unexpected diversity in polyubiquitin chain topology in vivo. The methodology described here provides a general tool for the large-scale analysis and characterization of protein ubiquitination.     

Ubiquitin metabolism in ts85 cells, a mouse carcinoma line that contains a thermolabile ubiquitin activating enzyme

Red blood cell-mediated microinjection was used to introduce radioiodinated ubiquitin into ts85 cells, a mouse cell line that contains a thermolabile ubiquitin-activating enzyme (E1). The proportion of ubiquitin present as histone conjugates, high molecular weight conjugates, and free molecules was then determined by gel electrophoresis and autoradiography. When ts85 cells were incubated at the nonpermissive temperature, 39.5 degrees C, high molecular weight conjugates accumulated. This unexpected result was confirmed by Western blot analyses. To determine whether ubiquitin conjugates formed under nonpermissive conditions or merely persisted after the temperature increase, ts85 cells were incubated at 39.5 degrees C to generate large amounts of conjugates and then shifted to 42 degrees C. The higher temperature resulted in a 25% reduction in conjugates, but upon return to 39.5 degrees C, the ubiquitin conjugates were restored to pre-42 degrees C amounts. Since all changes in ubiquitin conjugate levels occurred above 39.5 degrees C, ts85 cells can couple ubiquitin to cellular proteins even after prolonged culture at nonpermissive temperatures. Western blot analyses showed that less than 10% of the E1 molecules present in ts85 cells at 31 degrees C remained after 2 h at 39.5 degrees C. However, when 125I-ubiquitin was added to extracts from heated ts85 cells an apparent high molecular weight form of E1 and thiol ester adducts between ubiquitin and the E2 carrier proteins were detected by electrophoresis at 4 degrees C. Considering both in vivo and in vitro demonstrations that heated ts85 cells retain the ability to conjugate ubiquitin to endogenous proteins, considerable caution must be exercised in the design and interpretation of proteolysis experiments using this mutant cell line.     

Low oxygen sensing and balancing in plant seeds: a role for nitric oxide

Storage product accumulation in seeds of major crop species is limited by their low internal oxygen concentration. Adjustment of energy and storage metabolism to oxygen deficiency (hypoxia) in seeds is highly relevant for agriculture and biotechnology. However, the mechanisms of low-oxygen sensing and balancing remain a mystery. Here, it is shown that normal hypoxia in seeds of soybean (Glycine max) and pea (Pisum sativum) triggers a nitrite-dependent increase in endogenous nitric oxide (NO) concentrations. NO, in turn, reduces the oxygen consumption of seeds, generating a localized decrease in both ATP availability and biosynthetic activity. Increasing oxygen availability reduces endogenous NO concentrations, thereby abolishing mitochondrial and metabolic inhibition. This auto-regulatory and reversible oxygen balancing, via NO, avoids seed anoxia and suggests a key role for NO in regulating storage activity. This hypothesis is reinforced by changes in energy status (ATP:ADP ratio), steady-state metabolite concentrations and biosynthetic fluxes under NO treatment. The proposed mechanism of low-oxygen sensing and balancing in plants offers the prospect of a new field of study in crop biotechnology.     

Tissue- and stage-specific expression of a soybean (Glycine max L.) seed-maturation,biotinylated protein

A cDNA clone GmPM4 which encodes mRNA species in mature or dry soybean seeds was characterized. DNA sequence analysis shows that the deduced polypeptides have a molecular mass of 68 kDa. GmPM4 proteins have a relatively high amino acid sequence homology with a major biotinylated protein isolated from pea seeds, SBP65, but both of these proteins differ markedly from that of presently known biotin enzymes. The accumulation of GmPM4 mRNA is detectable in the leaf primodium and the vascular tissues of the hypocotyl-radicle axis of mature seeds, and the GmPM4 proteins are present at high levels in dry and mature soybean seeds, but not in fresh immature seeds. It degrades rapidly at the early stage of seed germination. These proteins are boiling-soluble and biotinylated when they are present endogenously in soybean seeds; however, the same recombinant protein expressed in Escherichia coli is boiling-soluble, but it is not biotinylated.     

Importance of methionine biosynthesis for Arabidopsis seed germination and seedling growth

Proteomics of Arabidopsis seeds revealed the differential accumulation during germination of two housekeeping enzymes. The first corresponded to methionine synthase that catalyses the last step in the plant methionine biosynthetic pathway. This protein was present at low level in dry mature seeds, and its level was increased strongly at 1-day imbibition, prior to radicle emergence. Its level was not increased further at 2-day imbibition, coincident with radicle emergence. However, its level in 1-day imbibed seeds strongly decreased upon subsequent drying of the imbibed seeds back to the original water content of the dry mature seeds. The second enzyme corresponded to S -adenosylmethionine synthetase that catalyses the synthesis of S -adenosylmethionine from methionine and ATP. In this case, this enzyme was detected in the form of two isozymes with different p I and M r. Both proteins were absent in dry mature seeds and in 1-day imbibed seeds, but specifically accumulated at the moment of radicle protrusion. Arabidopsis seed germination was strongly delayed in the presence of dl -propargylglycine, a specific inhibitor of methionine synthesis. Furthermore, this compound totally inhibited seedling growth. These phenotypic effects were largely alleviated upon methionine supplementation in the germination medium. The results indicated that methionine synthase and S -adenosylmethionine synthetase are fundamental components controlling metabolism in the transition from a quiescent to a highly active state during seed germination. Moreover, the observed temporal patterns of accumulation of these proteins are consistent with an essential role of endogenous ethylene in Arabidopsis only after radicle protrusion.     

Evidence of 4-Cl-IAA and IAA Bound to Proteins in Pea Fruit and Seeds

The auxins 4-chloroindole-3-acetic acid (4-Cl-IAA) and indole-3-acetic acid (IAA) occur naturally in pea vegetative and fruit tissues (Pisum sativum L.). Previous work has shown that 4-Cl-IAA can substitute for the seeds in the stimulation of pea pericarp growth, whereas IAA is ineffective. Both auxins are found as free acids and as low-molecular-weight conjugates from organic solvent-soluble extracts from pea fruit. Here we present evidence for an additional conjugated auxin species that was not soluble in organic solvent and yielded 4-Cl-IAA and IAA after strong alkaline hydrolysis, suggestive of auxin attachment to pea seed and pericarp proteins. The solvent-insoluble conjugated 4-Cl-IAA in young pericarp was on average 15-fold greater than solvent-soluble 4-Cl-IAA. The solvent-insoluble conjugated IAA was approximately half the levels reported for the solvent-soluble IAA fraction. To identify putative 4-Cl-IAA-bound proteins, polyclonal antibodies were raised to 4-Cl-IAA linked to bovine serum albumin protein (BSA). Immunoblots probed with anti-4-Cl-IAA-BSA antiserum detected three to four unique bands (32–40 kDa) in primarily maternal tissues, and a different set of protein bands were detected in mainly embryonic tissues (ca. 65–74 kDa in mature seed). 4-Cl-IAA and IAA were also identified from protein fractions separated by polyacrylamide gel electrophoresis using GC-MS. These data show that the majority of 4-Cl-IAA, the growth-active auxin in young pea pericarp, and significant levels of IAA are linked to protein fractions. Auxin-proteins may function in regulation of free bioactive 4-Cl-IAA and IAA levels, and/or 4-Cl-IAA or IAA may be targeted to specific proteins post-translationally to modify protein function or stability.     

Levels of aminoacyl-tRNA synthetases, tRNA nucleotidyltransferase and ATP in germinating lupin seeds

Transfer RNAs in dry lupin seeds are aminoacylated to a low extent (Kedzierski, W. and Pawe?kiewicz, J. (1977) Phytochemistry 16, 503-504) and are partly degraded at the acceptor terminus (Dziegielewski, T. and Pawe?kiewicz, J. (1977) Bull. Acad. Polon. Sci. Ser. Biol. 7, 4oo-435). Increase in the levels of tRNA aminoacylation and disappearance of defective tRNA molecules during seed germination are not accompanied by significant changes in the levels of phenylalanyl-, arginyl-, valyl-tRNA synthetases and tRNA nucleotidyltransferase. Additionally, no inhibitor of aminoacylation of valine tRNA has been detected in dry seeds. However, dry seeds contain very low ATP amounts, which increase dramatically during germination. The above results suggest that a very low ATP level is a factor limiting the aminoacylation and reparation of tRNA molecules at early stages of seed germination.     

Effects of cooling rate on seeds exposed to liquid nitrogen temperatures

The effect of cooling rate on seeds was studied by hydrating pea (Pisum sativum), soybean (Glycine max), and sunflower (Helianthus annuus) seeds to different levels and then cooling them to − 190°C at rates ranging from 1°C/minute to 700°C/minute. When seeds were moist enough to have freezable water (> 0.25 gram H₂O/gram dry weight), rapid cooling rates were optimal for maintaining seed vigor. If the seeds were cooled while at intermediate moisture levels (0.12 to 0.20 gram H₂O per gram dry weight), there appeared to be no effect of cooling rate on seedling vigor. When seeds were very dry (< 0.08 gram H₂O per gram dry weight), cooling rate had no effect on pea, but rapid cooling rates had a marked detrimental effect on soybean and sunflower germination. Glass transitions, detected by differential scanning calorimetry, were observed at all moisture contents in sunflower and soybean cotyledons that were cooled rapidly. In pea, glasses were detectable when cotyledons with high moisture levels were cooled rapidly. The nature of the glasses changed with moisture content. It is suggested that, at high moisture contents, glasses were formed in the aqueous phase, as well as the lipid phase if tissues had high oil contents, and this had beneficial effects on the survival of seeds at low temperatures. At low moisture contents, glasses were observed to form in the lipid phase, and this was associated with detrimental effects on seed viability.     

Immunolocalization of ubiquitin conjugates at Z-bands and intercalated discs of rat cardiomyocytes in vitro and in vivo.

Ubiquitin, a highly conserved 76-residue protein found in all eukaryotic cells, can be covalently bound to a wide variety of proteins in the nucleus, cytosol, cytoskeleton, and plasmalemma. This diversity of target proteins reflects a diversity of functions for ubiquitin conjugation. Previous studies have showed enhanced localization of ubiquitin conjugates to Z-bands of normal skeletal muscle and increased ubiquitination in atrophic muscles. These results have implicated a ubiquitin-mediated pathway in protein turnover and degradation in striated muscle. To investigate whether such a pathway might also exist in cardiac striated muscle, we used an affinity-purified polyclonal antibody (conjugate specific) and indirect immunofluorescence to localize ubiquitin conjugates in neonatal and adult rat cardiac myocytes both in vitro and in vivo. In both cultured myocytes and heart tissue, fluorescent ubiquitin conjugates were found in the nucleus as aggregates, in the cytoplasm in a striated pattern indicative of Z-bands, and in intercellular junctions at the intercalated discs between myocytes. Although the acceptor proteins and the physiological significance of ubiquitination at these locations are unknown, the targeting of ubiquitin to specific sites within the nucleus, myofibrils, and sarcolemma could provide a means for selective processing of individual components within these larger macromolecular assemblies, thus implying a regulatory role for ubiquitin conjugation in turnover or stability of proteins in the heart.     

Cellular content of ubiquitin and formation of ubiquitin conjugates during chicken spermatogenesis.

Ubiquitin was purified from chicken testis and its content, biosynthesis and formation of conjugates was determined in germinal cells at successive stages of spermatogenesis. Free ubiquitin increased markedly during spermatogenesis, reaching its maximum level in early spermatids. High levels of ubiquitin were still present in late spermatids but were not detectable in mature spermatozoa. Biosynthesis of ubiquitin occurred in vitro in a fraction containing meiotic and pre-meiotic cells, and during spermiogenesis, in early and late spermatids. The cellular content of free ubiquitin increased after ATP depletion, especially in early spermatids. Lysates of chicken testis cells, particularly those obtained from spermatids, were able to form nuclear (24 and 27 kDa) and extranuclear (55-90 kDa) ubiquitin conjugates in vitro. The presence of increasing levels of ubiquitin and ubiquitin conjugates in chicken spermatids may suggest a possible involvement of this protein in the marked changes of protein turnover, chromatin structure and cell-cell interactions that spermatids undergo during spermiogenesis.     

Ubiquitin-proteasome pathway and cellular responses to oxidative stress

The ubiquitin-proteasome pathway (UPP) is the primary cytosolic proteolytic machinery for the selective degradation of various forms of damaged proteins. Thus, the UPP is an important protein quality control mechanism. In the canonical UPP, both ubiquitin and the 26S proteasome are involved. Substrate proteins of the canonical UPP are first tagged by multiple ubiquitin molecules and then degraded by the 26S proteasome. However, in noncanonical UPP, proteins can be degraded by the 26S or the 20S proteasome without being ubiquitinated. It is clear that a proteasome is responsible for selective degradation of oxidized proteins, but the extent to which ubiquitination is involved in this process remains a subject of debate. Whereas many publications suggest that the 20S proteasome degrades oxidized proteins independent of ubiquitin, there is also solid evidence indicating that ubiquitin and ubiquitination are involved in degradation of some forms of oxidized proteins. A fully functional UPP is required for cells to cope with oxidative stress and the activity of the UPP is also modulated by cellular redox status. Mild or transient oxidative stress up-regulates the ubiquitination system and proteasome activity in cells and tissues and transiently enhances intracellular proteolysis. Severe or sustained oxidative stress impairs the function of the UPP and decreases intracellular proteolysis. Both the ubiquitin-conjugating enzymes and the proteasome can be inactivated by sustained oxidative stress, especially the 26S proteasome. Differential susceptibilities of the ubiquitin-conjugating enzymes and the 26S proteasome to oxidative damage lead to an accumulation of ubiquitin conjugates in cells in response to mild oxidative stress. Thus, increased levels of ubiquitin conjugates in cells seem to be an indicator of mild oxidative stress.     

The ubiquitin-proteasome system is a key component of the SUMO-2/3 cycle

Many proteins are regulated by a variety of post-translational modifications, and orchestration of these modifications is frequently required for full control of activity. Currently little is known about the combinatorial activity of different post-translational modifications. Here we show that extensive cross-talk exists between sumoylation and ubiquitination. We found that a subset of SUMO-2-conjugated proteins is subsequently ubiquitinated and degraded by the proteasome. In a screen for preferential SUMO-1 or SUMO-2 target proteins, we found that ubiquitin accumulated in purified SUMO-2 conjugates but not in SUMO-1 conjugates. Upon inhibition of the proteasome, the amount of ubiquitin in purified SUMO-2 conjugates increased. In addition, we found that endogenous SUMO-2/3 conjugates, but not endogenous SUMO-1 conjugates, accumulated in response to proteasome inhibitors. Quantitative proteomics experiments enabled the identification of 73 SUMO-2-conjugated proteins that accumulated in cells treated with proteasome inhibitors. Cross-talk between SUMO-2/3 and the ubiquitin-proteasome system controls many target proteins that regulate all aspects of nucleic acid metabolism. Surprisingly the relative abundance of 40 SUMO-2-conjugated proteins was reduced by proteasome inhibitors possibly because of a lack of recycled SUMO-2. We conclude that SUMO-2/3 conjugation and the ubiquitin-proteasome system are tightly integrated and act in a cooperative manner.     

Molecular characterization of the thermosensitive E1 ubiquitin-activating enzyme cell mutant A31N-ts20. Requirements upon different levels of E1 for the ubiquitination/degradation of the various protein substrates in vivo.

According to our current knowledge, protein ubiquitination involves three steps: activation of ubiquitin through formation of an energy-rich bond with an E1 ubiquitin-activating enzyme; and transfer of activated ubiquitin onto E2 ubiquitin-conjugating enzymes, which, in turn, alone, or in combination with E3 ubiquitin-protein ligase enzymes, transfer ubiquitin onto target proteins. A31N-ts20 cells are mouse embryo fibroblasts, thermosensitive for E1. We show here that: (a) the enzymatic activity of the enzyme is heat-inactivatable in vitro; and (b) a major mechanism responsible for E1 inactivation in vivo consists of accelerated destruction. Surprisingly, a >90% reduction in E1 abundance little alters the formation of the bulk of protein-ubiquitin conjugates when A31N-ts20 cells are grown at the nonpermissive temperature, indicating that cautious interpretation of results is required when studying ubiquitination of specific substrates using this cell line. Surprisingly, our data also indicate that, in vivo, ubiquitination of the various protein substrates in A31N-ts20 cells requires different amounts of E1, indicating that this mutant cell line can be used for unveiling the existence of differences in the intimate mechanisms responsible for the ubiquitination of the various cell proteins in vivo, and for providing criteria of reliability when developing in vitro ubiquitination assays for specific proteins.