Free ubiquitin is a non-histone protein of trout testis chromatin

The Role of Ubiquitin-Proteasome System and Mitophagy in the Pathogenesis of Parkinson's Disease

Parkinson's disease (PD) is a common neurodegenerative disease that is mainly in middle-aged people and elderly people, and the pathogenesis of PD is complex and diverse. The ubiquitin-proteasome system (UPS) is a master regulator of neural development and the maintenance of brain structure and function. Dysfunction of components and substrates of this UPS has been linked to neurodegenerative diseases such as Parkinson's disease and Alzheimer's disease. Moreover, UPS can regulate α-synuclein misfolding and aggregation, mitophagy, neuroinflammation and oxidative stress to affect the development of PD. In the present study, we review the role of several related E3 ubiquitin ligases and deubiquitinating enzymes (DUBs) on the pathogenesis of PD such as Parkin, CHIP, USP8, etc. On this basis, we summarize the connections and differences of different E3 ubiquitin ligases in the pathogenesis, and elaborate on the regulatory progress of different DUBs on the pathogenesis of PD. Therefore, we can better understand their relationships and provide feasible and valuable therapeutic clues for UPS-related PD treatment research.

Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response

Ubiquitin signaling is a conserved, widespread, and dynamic process in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization, or stability. To regulate this process, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, posttranslational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.

Probing the effects of double mutations on the versatile protein ubiquitin in Saccharomyces cerevisiae

Ubiquitin is an indispensable protein of eukaryotic origin with an extraordinarily high degree of sequence conservation. It is used to tag proteins post-translationally and the process of ubiquitination regulates the activity of the modified proteins or drives them for degradation. Double mutations produce varied effects in proteins, depending on the structural relationship of the mutated residues, their role in the overall structure and functions of a protein. Six double mutants derived from the ubiquitin mutant UbEP42, namely S20F-A46S, S20F-L50P, S20F-I61T, A46S-L50P, A46S-I61T, and L50P-I61T, have been studied here to understand how they influence the ubiquitination related functions, by analysing their growth and viability, Cdc28 levels, K-48 linked polyubiquitination, UFD pathway, lysosomal degradation, endosomal sorting, survival under heat, and antibiotic stresses. The double mutation L50P-I61T is the most detrimental, followed by S20F-I61T and A46S-I61T. The double mutations studied here, in general, make cells more sensitive than the wild type to one or the other stress. However, the excessive negative effects of L50P and I61T are compensated under certain conditions by S20F and A46S mutations. The competitive inhibition produced by these substitutions could be used to manage certain ubiquitination associated diseases.

Purification and antimicrobial function of ubiquitin isolated from the gill of Pacific oyster, Crassostrea gigas

An antimicrobial polypeptide was purified from an acidified gill extract of Pacific oyster (Crassostrea gigas) by C(18) reversed-phase HPLC. The purified polypeptide had a molecular weight of 8471Da containing 74 amino acid residues. Comparison of the obtained N-terminal sequences with those of others revealed that it was identical to ubiquitin reported from other species and named cgUbiquitin. cgUbiquitin showed broad potent antimicrobial activity against Gram-positive and -negative bacteria including Streptococcus iniae and Vibrio parahemolyticus (minimal effective concentrations, 7.8 and 9.8μg/mL), respectively, without hemolytic activity. The cgUbiquitin cDNA was identified from an expressed sequence tag (EST) library of oyster gill as a precursor form, encoding ubiquitin consisting of 76 amino acids fused to ribosomal protein of S27. Although the cgUbiquitin precursor mRNA was expressed at the intermediate level in the gill, the mRNA was significantly up-regulated at 48h post injection with Vibrio sp. Analysis of the cgUbiquitin C-terminus by carboxypeptidase B treatment and comparison of the retention times revealed that cgUbiquitin lacks the terminal Gly-Gly doublet and ends in an C-terminal Arg residue which might be related to antimicrobial activity. Study of the kinetics of killing and membrane permeabilization showed that this peptide was not membrane permeable and acted through a bacteriostatic process. According to the homology modeling, this peptide is composed of three secondary structural motifs including three α-helices and four β-strands separated by 7 loops regions. Our results indicate that cgUbiquitin might be related to the innate immune defenses in the Pacific oyster and this is the first report for antimicrobial function of ubiquitin isolated from any oyster species.

Ubiquitin genes in rainbow trout (Oncorhynchus mykiss)

Ubiquitin is a small protein involved in intracellular proteolysis. It is highly conserved throughout eukaryotic phyla and has been detected in such diverse species as yeast, barley, Drosophila and man. A previous study showed that chromatin of rainbow trout testis contains free ubiquitin with a sequence similar to that of other phyla. In the present study, which focused on rainbow trout but included eleven other species, it is shown that fish ubiquitin genetic organisation and expression are similar to those of other phylogenetic groups through the following set of observations: (a) Multiple loci were detected, (b) These loci encode repeats of ubiquitin, (c) Although the DNA sequences are not conserved, the encoded amino acid sequences are fully conserved, (d) The expression of ubiquitin was influenced by cell culture conditions and viral infection.

The ubiquitin system in gametogenesis

Ubiquitin is a ubiquitous and highly conserved protein of 76 amino acid residues, that can be covalently attached to cellular acceptor proteins. The attachment of ubiquitin to target proteins is achieved through a multi-step enzymatic pathway, which involves activities of ubiquitin-activating E1 enzymes, ubiquitin-conjugating E2 enzymes, and ligating E3 enzymes. Mono- or poly-ubiquitination of proteins can lead to protein degradation or modification of protein activity. Many components of the complex ubiquitin system show remarkable evolutionary conservation, from yeast to mammalian species. The ubiquitin system is essential to all eukaryotic cells. Among others, several signal transduction cascades show involvement of the ubiquitin system, but there are currently little data supporting a specific role of the ubiquitin system in hormonal control of reproduction. Interestingly, during gametogenesis, many specialized and important aspects of the ubiquitin system become apparent. Components of the ubiquitin system appear to be involved in different steps and processes during gametogenesis, including control of meiosis, and reorganization of chromatin structure.

Nature and role of proteasomes in maturation of fish oocytes

The proteasome is an essential component of the proteolytic pathway in eukaryotic cells and is responsible for the degradation of most cellular proteins. Proteasomes are sorted into two types, 20S and 26S. The 20S proteasome forms the catalytic core of the 26S proteasome. The 26S proteasome is involved in the ubiquitin-dependent protein degradation pathway. Cyclins and cdk inhibitors or c-mos products, proteins critical to the regulation of the cell cycle, are known to be degraded by the ubiquitin pathway. Thus the 26S proteasome is thought to be involved in the regulation of cell cycle events. This review focuses on advances in the study of the biochemical properties and functions of the 20S and 26S proteasomes in the fish meiotic cell cycle.

Serological evidence and amino acid sequence of ubiquitin-like protein isolated from coelomic fluid and cells of the earthworm Eisenia fetida andrei

1. A small protein of M(r) 10 kDa has been isolated by reverse-phase chromatography of the basic proteins contained in the coelomic fluid and cell lysate of the earthworm Eisenia fetida andrei. 2. The protein crossreacted in dot-blot with an anti-bovine ubiquitin antiserum. 3. Its N-terminal primary structure was determined by automatic Edman degradation on 26 consecutive amino acids and showed 69% (based on the 26 amino acids) or 82% (based on the first 19 consecutive amino acids) identity with many ubiquitins and similar charge and hydrophobicity profiles and secondary structure conformation.

Structure of the macronuclear polyubiquitin gene in Euplotes

The hypotrichous ciliate, Euplotes eurystomus, contains both a transcriptionally inactive micronucleus (MIC) and a transcriptionally active macronucleus (MAC) in the same cell. MAC DNA is small (0.5-20 kb), linear and highly amplified. Each DNA fragment consists of two telomeres, a single coding region, and the necessary control elements to regulate gene transcription and replication. The polyubiquitin gene consists of 898 bp, plus 28 bp of double-stranded and 14 bases of single-stranded DNA of the telomeric repeat G4T4 at each end. The coding region exists as three copies of the ubiquitin gene (690 bp) fused in a head-to-tail arrangement as in other organisms. The stop codon is TAA, as in other Euplotes genes, and is not the rare glutamine codon used in most other ciliates. The 3' nontranslated region contains two presumptive poly(A) addition sites; the 5' nontranslated region possesses two putative TATA boxes, several imperfect direct and inverted repeats, and a possible origin of replication. Nucleosome positioning studies reveal four tightly packed nucleosomes and a non-nucleosomal area containing the probable 5' control region as well as part of the coding region. The 5' area does not contain any DNAse I hypersensitive sites. Although the telomeres are protected from exonuclease digestion, they are not as well protected as Oxytricha telomeres against endonucleases and cleavage by methidium propyl Fe2+ EDTA.

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.

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 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.

Structure of ubiquitin refined at 1.8 A resolution

The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond lengths and bond angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 1.5 degrees, respectively. A total of 58 water molecules per molecule of ubiquitin are included in the final model. The last four residues in the molecule appear to have partial occupancy or large thermal motion. The overall structure of ubiquitin is extremely compact and tightly hydrogen-bonded; approximately 87% of the polypeptide chain is involved in hydrogen-bonded secondary structure. Prominent secondary structural features include three and one-half turns of alpha-helix, a short piece of 3(10)-helix, a mixed beta-sheet that contains five strands, and seven reverse turns. There is a marked hydrophobic core formed between the beta-sheet and alpha-helix. The molecule features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns.

The human ubiquitin gene family: structure of a gene and pseudogenes from the Ub B subfamily

An ubiquitin cDNA clone was isolated from a human liver cDNA library. This clone contained two complete, and a portion of a third, ubiquitin coding sequences joined head to tail with no spacer peptides. Screening a human genomic library with a probe derived from the coding region of this cDNA identified a large number of cross-hybridising clones. Differential screening of these genomic clones with the 3' non-coding region of the cDNA identified three different 3'-positive clones. Sequence analysis of these three clones revealed: a gene corresponding to the cDNA containing an intron in the 5' non-coding region and coding for three direct repeats of mature ubiquitin, and two related pseudogenes which appear to have arisen by reverse transcription and insertion into the genome. However, one pseudogene contains two repeats of the ubiquitin coding sequence, while the other contains only one. Hybridisation analysis of restricted human genomic DNA suggests the presence of one other closely related gene within the genome.

Role of ubiquitin conformations in the specificity of protein degradation: iodinated derivatives with altered conformations and activities

Three iodinated derivatives of ubiquitin have been synthesized and these derivatives have been characterized in the ubiquitin-dependent protein degradation system. With chloramine-T as the oxidant, a derivative containing monoiodotyrosine is formed in the presence of 1 M KI and a derivative containing diiodotyrosine is produced in the presence of 1 mM KI. These derivatives exhibit phenolate ionizations at pH 9.2 and 7.9 with absorbance maxima at 305 and 314 nm, respectively. In addition to modification of the tyrosine residue, these conditions lead to the oxidation of the single methionine residue and iodination of the single histidine residue [M.J. Cox, R. Shapira, and K.D. Wilkinson (1986) Anal. Biochem. 154, 345-352]. Iodination of ubiquitin under these conditions renders the protein sensitive to hydrolysis by trypsin and results in an enhanced susceptibility to alcohol-induced helix formation. When the derivatives are tested in the ATP: pyrophosphate exchange reaction catalyzed by the ubiquitin adenylating enzyme, they are found to exhibit activity comparable to the native protein. When these derivatives are tested for the ability to act as a cofactor in the ubiquitin-dependent protein degradation system, they are both found to support a rate of protein degradation that is twice that of native ubiquitin. At high concentrations of derivatives, the rate of protein degradation is inhibited, while the steady state level of conjugates increases. Thus, the free derivatives inhibit the protease portion of the reaction, but are fully active in the activation and conjugation portions of the reaction. With iodine as the modification reagent, monoiodination of tyrosine is the predominant reaction. This derivative exhibits activity similar to native ubiquitin. Thus, it appears that modification of the histidine residue is responsible for the increased activity of the more highly iodinated derivatives. The enzymes of the system must recognize different portions of the ubiquitin structure, or different conformations of ubiquitin that are affected by the iodination of the histidine residue. These results suggest a conformational change of the ubiquitin molecule may be important in determining the rate and specificity of proteolysis.

Alcohol-induced conformational changes of ubiquitin

Ubiquitin has been found to be soluble in ethylene glycol and alcohols as the perchlorate or hydrochloride salt. When the effect of alcohol on the structure of ubiquitin is examined, two reversible conformational transitions are observed. Upon lowering the dielectric constant of aqueous alcohol solutions of ubiquitin from 80 to 45, the native structure of ubiquitin is converted to a form consistent with 50% helical structure. This conformational change results in a change in exposure to solvent of the single methionine and the single tyrosine residues of ubiquitin. In agreement with crystallographic results, these residues are buried in the native conformation but become fully exposed to solvent upon undergoing this transition. Further lowering of the dielectric constant to 20 results in the accumulation of a conformation with almost complete helical structure. Thus, hydrophobic interactions cause facile conformational changes in the ubiquitin structure. These results are discussed in terms of a preferential solvation model. It is shown that the results obtained with different alcohols can be normalized by the use of a dielectric constant scale. This normalization corrects for the different molar volumes of different alcohols, allows comparison of results obtained with different alcohols, and should be useful in studying this phenomenon with different proteins.

Structure and expression of ubiquitin genes in higher plants

cDNA clones encoding ubiquitin were isolated from a barley leaf cDNA library using a mammalian ubiquitin cDNA clone as probe. The nucleotide sequence of one of the clones codes for 2.2 perfect repeats of the 76-amino-acid-long ubiquitin protein with an extra lysine residue at the C-terminus. The barley ubiquitin amino acid sequence differs from the animal sequence at three positions and from the yeast sequence at two positions. The ubiquitin poly(precursor) are coded by a multigene family with 8-10 genes that produce four or five different size messengers between 700 and 2000 nucleotides in length. The large poly(A)-rich RNAs are constitutively expressed in vegetative tissues whereas the 700-nucleotide messenger(s) were only detected in tissues containing dividing cells.

Tryptic peptide mapping of ubiquitin and derivatives using reverse-phase high performance liquid chromatography

The conditions for tryptic digestion and subsequent peptide mapping of the ATP-dependent proteolysis cofactor ubiquitin and its derivatives are described. In aqueous solution, the native ubiquitin which is composed of 76 amino acids undergoes only a single cleavage at arginine-74. Full digestion of ubiquitin was obtained in 6.5 M urea, although cleavages at lysine-33 and arginine-74 were slow. Peptide mapping was achieved by reverse-phase high-performance liquid chromatography with a C18 column using a trifluoroacetic acid/triethylamine buffer system and acetonitrile as eluants. The peptides, separated using a linear gradient, were identified by amino acid analysis. Derivatives analyzed by this method include oxidized, monoiodotyrosyl, and diiodotyrosyl ubiquitin. This technique will be useful in examining peptides of chemically modified ubiquitin with respect to extent and specificity of modification. In addition, this technique will be useful in comparing ubiquitin peptides of different organisms.

Cell surface molecule associated with lymphocyte homing is a ubiquitinated branched-chain glycoprotein

Partial amino acid sequence analysis of a purified lymphocyte homing receptor demonstrates the presence of two amino termini, one of which corresponds precisely to the amino terminus of ubiquitin. This observation extends the province of this conserved polypeptide to the cell surface and leads to a proposed model of the receptor complex as a core polypeptide modified by glycosylation and ubiquitination. Independent antibodies to ubiquitin serve to identify additional cell surface species, an indication that ubiquitination of cell surface proteins may be more general. It is proposed that functional binding of lymphocytes to lymph node high endothelial venules might involve the ubiquitinated region of the receptor; if true, cell surface ubiquitin could play a more general role in cell-cell interaction and adhesion.

Investigations of primary and secondary structure of porcine ubiquitin. Its N epsilon-acetylated lysine derivative

N epsilon-acetylation in vitro of internal lysyl residues of Ub by p-nitro-phenyl acetate at pH 8.0 was performed. The position of acetylation sites are determined. (e.g. Fully acetylated: Lys-6, Lys-11 and Lys-33; partially free internal lysines: Lys-27, Lys-29; Lys-48 and probably Lys-63.) 55 cycles Edman degradation were performed and the first 53 N-terminal residues were identified. Secondary structural studies of ubiquitin have been carried out using the circular dichroism (CD) technique. No changes are noted upon heating to 100 degrees C at neutral pH even in the presence of 8 M urea but in 6 M guanidine-HCl extensive modification results. Ubiquitin with an average of 4.4 of its 7 lysines in the N epsilon-acetyl form shows little deviation from native protein. After reduction with dithiothreitol and subsequent removal of the mercaptan, significant changes in the secondary structure are noted. Circular dichroic measurements of ubiquitin indicated an alpha-helical content of about 10% whereas the secondary structural predictions of Chou and Fasman suggest a level of about 45%.

Three-dimensional structure of ubiquitin at 2.8 A resolution

The three-dimensional structure of ubiquitin has been determined at 2.8 A resolution. X-ray diffraction data for the native protein and derivatives were collected with an automated diffractometer. Phases were obtained by use of a single isomorphous mercuric acetate derivative. The molecule contains a pronounced hydrophobic core. Prominent secondary structural features include three and one-half turns of alpha-helix, a mixed beta-sheet that contains four strands, and seven reverse turns. The histidine, tyrosine, and two phenylalanine residues are located on the surface of the molecule.

Localization of lysines acetylated in ubiquitin reacted with p-nitrophenyl acetate

The protein ubiquitin undergoes extensive N epsilon-acetylation of some of its seven lysine residues when reacted with p-nitrophenyl acetate. Lysines 27 and 29 show little reactivity whereas residue 6 is the most readily acetylated. Residues 11, 33, 48, and 63 show intermediate reactivities.

The large scale purification of ubiquitin from human erythrocytes

A simple, reproducible method for the large-scale purification of active ubiquitin from human erythrocytes is described. Erythrocytes contain 100 micrograms free ubiquitin per cc of packed cells, of which 44% can be recovered in homogeneous form by a combination of heat treatment, ammonium sulfate fractionation, and ion exchange chromatography.

Purification and characterization of ubiquitin from mammalian testis

Ubiquitin was extracted from testis of 4 mammals and purified to homogeneity by gel filtration chromatography. Amino acid compositions and NH2-terminal sequences were found to be identical in the 4 species and with calf thymus ubiquitin. Ubiquitin conformation was shown to be very sensitive to oxidation. Improved methods for radioimmunoassay of ubiquitin in tissue extracts are also discussed.

The ubiquitin-mediated proteolytic pathway and mechanisms of energy-dependent intracellular protein degradation

In this review we briefly describe the lysosomal system, consider the evidence for multiplicity of protein degradation pathways in vivo, discuss in detail the ubiquitin-mediated pathway of intracellular ATP-dependent protein degradation, and also the possible significance of ubiquitin-histone conjugates in chromatin. For detailed discussions of the various characteristics and physiological roles of intracellular protein breakdown, the reader is referred to earlier reviews [1-7] and reports of recent symposia [8-10]. Information on the ubiquitin system prior to 1981 was described in an earlier review [11]. Hershko has briefly reviewed more recent information [12].

High mobility group nonhistone chromosomal proteins of the developing sea urchin embryo

The high mobility group or HMG proteins are nonhistone chromosomal proteins that have been found in relatively high amounts in nuclei of many tissues. A number of studies have shown that some of these proteins are preferentially associated with actively transcribed regions of the genome and may play a role in maintaining these regions in an active state. In this study, we undertook an investigation of the high mobility group proteins from the sea urchin, Stronglyocentrotus purpuratus. Initially the putative sea urchin HMGs were extracted from isolated nuclei of hatching blastula-stage embryos with 5% perchloric acid (PCA). The major proteins in this extract were characterized according to their electrophoretic mobility, amino acid composition, and association with isolated deoxyribonucleoprotein particles. The results indicate there is only one "major" sea urchin HMG protein, termed P2 in this paper. An estimate of the amount of P2 in relation to the inner histones, however, was low compared to what has been found for other HMG proteins. Of the other major 5% PCA-extractable proteins, one was identified as the cleavage stage H1. Another protein apparently resulted from H3 contamination in the 5% PCA extract, and the fourth major protein did not have all the characteristics of an HMG. In particular, it was not found associated with nucleosomal particles. The HMG proteins from other developmental stages were then examined. Five percent PCA extracts of nuclei from unfertilized eggs, 2-cell, 16-cell, hatching blastula, gastrula, and pluteus stages were analyzed on SDS- and acetic acid-urea gels. This analysis indicated that P2 exists in two different forms differing slightly in charge. The less basic form was found in the egg, 2-cell and 16-cell extracts. At the hatching blastula stage, both forms were present and by pluteus stage, the more basic form predominated. It appears that P2 is undergoing a developmental change from a less to more basic form. The presence of P2 in the 5% PCA extract of egg nuclei is proof that P2 does not initially appear sometime during embryogenesis but is already in the egg nucleus prior to fertilization.

Isolation, characterization, and postsynthetic modifications of tetrahymena high mobility group proteins

We have isolated four major high mobility group (HMG) proteins designated A, B, C, and D, together with ubiquitin from the ciliate protozoan Tetrahymena. These four HMG proteins are integral structural components of macronuclear nucleosomes. The proteins exhibit solubility properties, chromatographic behavior on carboxymethylcellulose, electrophoretic mobilities on various gel systems, and amino acid compositions similar to those of their mammalian counterparts. HMG-A is the largest, most acidic protein of the group and is phosphorylated in vivo at specific serine residues. HMG-B is both phosphorylated at serine residues and ADP ribosylated. HMG-C is not phosphorylated but is ADP ribosylated. HMG-D, the smallest, most basic protein of the group possesses an unusually high content of serine and threonine residues, and it is highly phosphorylated at both serine and threonine positions in the polypeptide chain.

The effect of isoproterenol and hydroxyurea on the presence of ubiquitin and protein A24 in the rat salivary gland

The in vivo administration of hydroxyurea for 12 h counteracts DNA synthesis and cell cycling stimulated by 72 h of isoproterenol treatment in rat salivary gland, as determined by fluorescence-activated flow cytometry. Hydroxyurea has little effect on [3H]leucine incorporation (protein synthesis) of the nuclear proteins soluble in 0.35 M NaCl, when examined by polyacrylamide gel chromatography and autoradiography from electrostatically sorted nuclei of (G0 + G1) and (G2 + M) phases of the in vivo cell cycle. Differential incorporation of [3H]leucine into nuclear proteins was observed during various phases of the cell cycle. Proteins 'X' and 'Z', observed in stained gel chromatographs of the 0.35 M NaCl-soluble nuclear proteins, were identified by biochemical analyses as ubiquitin and protein A24, respectively. Ubiquitin appeared transiently while A24 increased in gel chromatograms concomitant with progressive quiescence of the salivary gland induced by hydroxyurea.

Effect of high mobility group nonhistone proteins HMG-20 (ubiquitin) and HMG-17 on histone deacetylase activity assayed in vitro

We have used a method previously described by Reeves and Candido (1) to partially release histone deacetylase from cell nuclei together with putative regulators of the enzyme. Histone deacetylase released from testis cell nuclei and its putative regulators were separated by gel filtration in Sepharose 6B. A peak of low molecular weight contains a heat-stable factor that stimulate histone deacetylase in vitro. Many of the properties of the activator coincide with those of the protein HMG-20 (ubiquitin). Ubiquitin isolated from testis cell nuclei stimulated histone deacetylase in vitro. It has been suggested that HMG-17 partially inhibits histone deacetylase in Fried cell nuclei (2). In our system, HMG-17 shows no inhibitory effect on histone deacetylase activity

Ubiquitin - protein conjugates

The data available at present indicates there are three distinct functions of ubiquitin, two of which are related to protein conjugation. The first of these has been extensively studied by our laboratory and others interested in nucleosomes and changes in chromatin states. The ubiquitin-histone (Ub-2A, Ub-2B) conjugation reaction now appears to be a very dynamic process. In the deconjugation (lyase) reaction, both the histone 2A and the ubiquitin are left intact and in a form which makes possible ready reconjugation. Accordingly, this may be a mechanism for "moment-to-moment" Control of the genome. The second function in which ubiquitin is conjugated involves proteolytic activity. This activity is correlated with protein turnover. In this process, the ubiquitin-protein conjugate apparently serves as a "signal" for the protease cleavage of the protein. The released ubiquitin is also intact and is probably available for reconjugation. In the third function, ubiquitin was suggested to serve as a "hormone". The studies thus far have been carried out primarily on induction of T- and B-lymphocytes, reduction or delay of Coombs' positivity and reduction of spleen weight. The precise physiological role of this reported function is still unclear, particularly because the ubiquitin used was probably not the physiologically active form.

Structural studies of the non-histone chromosomal proteins HMG-T and H6 from trout testis

Trout testis contains two proteins of the high mobility group H6 and HMG-T that have been implicated in the structure of active chromatin. Protein H6 was studied by high resolution proton NMR and by circular dichroism and showed no evidence of secondary or tertiary structure formation in free solution. At low ionic strength protein H6 binds to DNA by a weak interaction in the N-terminal region between residues 10 and 35. Proteins H6 therefore behaves structurally like the homologous calf-thymus high-mobility-group proteins HMG-14 and HMG-17. Salt addition to solutions of protein HMG-T results in secondary and tertiary structure formation that is accompanied by aggregation. Circular dichroism shows that the helical content of protein HMG-T (approximately equal to 9%) is very much less than that of the homologous calf thymus proteins HMG-1 and HMG-2. At low ionic strength protein HMG-T precipitates DNA due to the formation of large scale aggregates that disperse only when the protein is released at approximately equal to 0.35 M NaCl. The NMR spectrum of the aggregated state does not show the presence of a large number of free acidic residues, in contrast to spectra of soluble complexes of HMG-1 and DNA at the same ionic strengths. It is concluded that HMG-T lacks the highly acidic domain found in HMG-1 (and HMG-2) that remains free from DNA under these conditions. It is concluded that the entire chain of HMG-T binds to DNA. There are therefore major structural differences between HMG-T and the homologous calf thymus proteins.