Prosomes exist in plant cells too

Purification of 26S Proteasomes and Their Subcomplexes from Plants

The 26S proteasome is a highly dynamic, multisubunit, ATP-dependent protease that plays a central role in cellular housekeeping and many aspects of plant growth and development by degrading aberrant polypeptides and key cellular regulators that are first modified by ubiquitin. Although the 26S proteasome was originally enriched from plants over 30 years ago, only recently have significant advances been made in our ability to isolate and study the plant particle. Here, we describe two robust methods for purifying the 26S proteasome and its subcomplexes from Arabidopsis thaliana; one that involves conventional chromatography techniques to isolate the complex from wild-type plants, and another that employs the genetic replacement of individual subunits with epitope-tagged variants combined with affinity purification. In addition to these purification protocols, we describe methods commonly used to analyze the activity and composition of the complex.

HcPro, a multifunctional protein encoded by a plant RNA virus, targets the 20S proteasome and affects its enzymic activities

The proteasome is a multicatalytic complex involved in many cellular processes in eukaryotes, such as protein and RNA turnover, cell division, signal transduction, transcription and translation. Intracellular pathogens are targets of its enzymic activities, and a number of animal viruses are known to interfere with these activities. The first evidence that a plant virus protein, the helper component-proteinase (HcPro) of Lettuce mosaic virus (LMV; genus Potyvirus), interferes with the 20S proteasome ribonuclease is reported here. LMV infection caused an aggregation of the 20S proteasome to high-molecular mass structures in vivo, and specific binding of HcPro to the proteasome was confirmed in vitro using two different approaches. HcPro inhibited the 20S endonuclease activity in vitro, while its proteolytic activities were unchanged or slightly stimulated. This ability of HcPro, a pathogenicity regulator of potyviruses, to interfere with some of the catalytic functions of the 20S proteasome suggests the existence of a novel type of defence and counter-defence interplay in the course of interaction between potyviruses and their hosts.

Biochemical identification of proteasome-associated endonuclease activity in sunflower

Proteasomes have been purified from sunflower hypocotyles. They elute with a molecular mass of 600 kDa from gel filtration columns and two-dimensional gel electrophoresis indicates that the complex contains at least 20 different protein subunits. Peptide microsequencing revealed the presence of four subunits homologous to subunits Beta2, Beta6, Alpha5 and Alpha6 of plant proteasomes. These proteasomes have chymotrypsin-like activity and the highly purified fraction of this complex is associated with an endonuclease activity hydrolyzing Tobacco mosaic virus RNA and Lettuce mosaic virus RNA with a cleavage pattern showing fragments of well-defined size. This is the first evidence of a RNA endonuclease activity associated with plant proteasomes.

Molecular organization of the 20S proteasome gene family from Arabidopsis thaliana

The 20S proteasome is the proteolytic complex in eukaryotes responsible for degrading short-lived and abnormal intracellular proteins, especially those targeted by ubiquitin conjugation. The 700-kD complex exists as a hollow cylinder comprising four stacked rings with the catalytic sites located in the lumen. The two outer rings and the two inner rings are composed of seven different alpha and beta polypeptides, respectively, giving an alpha7/beta7/beta7/alpha7 symmetric organization. Here we describe the molecular organization of the 20S proteasome from the plant Arabidopsis thaliana. From an analysis of a collection of cDNA and genomic clones, we identified a superfamily of 23 genes encoding all 14 of the Arabidopsis proteasome subunits, designated PAA-PAG and PBA-PBG for Proteasome Alpha and Beta subunits A-G, respectively. Four of the subunits likely are encoded by single genes, and the remaining subunits are encoded by families of at least 2 genes. Expression of the alpha and beta subunit genes appears to be coordinately regulated. Three of the nine Arabidopsis proteasome subunit genes tested, PAC1 (alpha3), PAE1 (alpha5) and PBC2 (beta3), could functionally replace their yeast orthologs, providing the first evidence for cross-species complementation of 20S subunit genes. Taken together, these results demonstrate that the 20S proteasome is structurally and functionally conserved among eukaryotes and suggest that the subunit arrangement of the Arabidopsis 20S proteasome is similar if not identical to that recently determined for the yeast complex.

Changes in the amount and distribution of prosomal subunits during the differentiation of U937 myeloid cells: high expression of p23K

Prosomes (Proteasomes/Multicatalytic proteinase (MCP)-complexes) are protein particles built of 28 subunits in variable composition, having proteinase activity. We have studied the changes in prosomal subunits p29K, p31K and the highly expressed p23K during the differentiation of U937 cells. Control cells had little prosomal subunit p31K in the cytoplasm, while p29K antigen was detected in both the nucleus and cytoplasm; more p23K antigen was found in the cytoplasm than in the nucleus. Flow cytometry demonstrated a biphasic intracellular decrease in prosomes during differentiation induced by phorbol-myristic-acetate (PMA) and retinoic acid plus 1,25-dihydroxycholecalciferol (RA + VD). p23K and p29K decreased both in the cytoplasm and the nucleus of differentiated cells, though the p23K antigen was concentrated near vesicles and the plasma membrane in PMA-induced cells. The p31K antigens disappeared from RA + VD-induced cells, while in PMA-induced cells, cytoplasmic labelling was unchanged and nuclear labelling was increased. Small amounts of prosomal proteins p23K and p29K were found on the outer membrane of un-induced cells. While there was no labelling on the outer membrane of RA + VD-induced cells, p23K protein increased on the plasma membrane of PMA-induced cells. The prosome-like particle protein p21K was not present to any significant extent in the intracellular compartment of control or induced cells; however, p21K was detected on the outer surface of control cells and was increased only in PMA-induced cells. The culture medium of control and induced cells contained no p21K, p23K, p29K or p31K. RA + VD seemed to induce a general decrease of prosomal subunits within the cells and at the outer surface, whereas PMA caused a migration toward the plasma membrane and an increase at the outer surface. These changes in the distribution and type of prosomes in RA + VD- and PMA-induced cells indicate that prosomes may play a part in differentiation, especially p23K which is the most highly expressed protein among those studied and presents the more important changes.

An Arabidopsis gene homologous to mammalian and insect genes encoding the largest proteasome subunit

A gene encoding a protein with extensive homology to the largest subunit of the multicatalytic proteinase complex (proteasome) has been identified in Arabidopsis thaliana. This gene, referred to as AtPSM30, is entirely encompassed within a previously characterized radiation-induced deletion, which may thus provide the first example of a proteasome null mutation in a higher eukaryote. However, the growth rate and fertility of Arabidopsis plants do not appear to be significantly affected by this mutation, even though disruption experiments in yeast have shown that most proteasome subunits are essential. Analysis of mRNA levels in developing seedlings and mature plants indicates that expression of AtPSM30 is differentially regulated during development and is slightly induced in response to stress, as has been observed for proteasome genes in yeast, Drosophila, and mammals. Southern blot analysis indicates that the Arabidopsis genome contains numerous sequences closely related to AtPSM30, consistent with recent reports of at least two other proteasome genes in Arabidopsis. A comparison of the deduced amino acid sequences for all proteasome genes reported to date suggests that multiple proteasome subunits evolved in eukaryotes prior to the divergence of plants and animals.

Disruption of prosomes by some bivalent metal ions results in the loss of their multicatalytic proteinase activity and cancels the nuclease resistance of prosomal RNA

Prosomes are ribonucleoprotein particles constituted by a variable set of about 20 proteins found associated with untranslated mRNA. In addition, they contain a small RNA, the presence of which has been an issue of controversy for a long time. The intact particles have a multicatalytic proteinase (MCP) activity and are very stable; we have never observed autodigestion of the particle by its intrinsic proteinase activity. Surprisingly it was found that Zn2+ and Cu2+ ions at concentrations of 0.1-1 mM disrupt the prosome particles isolated from HeLa cells and duck erythroblasts and abolish instantaneously its MCP activity, without altering the two-dimensional electrophoretic pattern of the constituent proteins. Fe2+, however, seems to induce autodegradation rather than dissociation of the prosome constituents. Most interestingly, protein or oligopeptide substrates protect the particle and its proteinase activity from disruption by Zn2+ or Cu2+. Nuclease-digestion assays reveal that the prosomal RNA, which is largely resistant in the intact particle, becomes digestible after dissociation of prosomes by Zn2+. These data give, for the first time, unambiguous proof of the presence of an RNA in the particle. Furthermore, they demonstrate a structure-function relationship between the complex and its enzyme activity, which seems to be based on the particle as an entity and not on the single constituent proteins.

Prosomes and their multicatalytic proteinase activity

Prosomes were first described as being mRNA-associated RNP (ribonucleoprotein) particles and subcomponents of repressed mRNPs (messenger ribonucleoprotein). We show here that prosomes isolated from translationally inactive mRNP have a protease activity identical to that described by others for the multicatalytic proteinase complex (MCP, 'proteasome'). By RNase or non-ionic detergent treatment, the MCP activity associated with repressed non-globin mRNP from avian erythroblasts, sedimenting at 35 S, could be quantitatively shifted on sucrose gradients to the 19-S sedimentation zone characteristic of prosomes, which were identified by monoclonal antibodies. The presence of small RNA in the enzymatic complex was shown by immunoprecipitation of the protease activity out of dissociated mRNP using a mixture of anti-prosome monoclonal antibodies; a set of small RNAs 80-120 nucleotides long was isolated from the immunoprecipitate. Furthermore, on CsCl gradients, colocalisation of the MCP activity with prosomal proteins and prosomal RNA was found, and no difference in the prosomal RNA pattern was observed whether the particles were fixed or not prior to centrifugation. These data indicate that the MCP activity is a property of prosomes, shown to be in part RNP and subcomplexes of in vivo untranslated mRNP. A hypothesis for the role of the prosome-MCP particles in maintaining homeostasis of specific protein levels is proposed.

Co-purification of a small RNA species with multicatalytic proteinase (proteasome) from rat liver

Previous studies have come to different conclusions about the presence of RNA in particles known variously as prosomes, proteasomes or multicatalytic proteinase (MCP). To determine the reason for this, MCP was isolated from rat liver by 4 different purification protocols. One major band of RNA, about 80 nucleotides in length, co-purified in all preparations. The amount of RNA detected was less than one molecule per MCP particle suggesting that there may be more than one population of MCP in rat liver cells.

Cell-specific accumulation of Drosophila proteasomes (MCP) during early development

The proteasome (MCP) is a high relative molecular mass multicatalytic proteinase complex composed of nonidentical protein subunits. We have investigated the cellular distribution of the enzyme complex during Drosophila embryogenesis using the proteasome specific antibodies N19-35 and N19-28 for immunocytology. Antibody staining of whole-mount embryos shows that during embryogenesis proteasomes are present in proliferating cells and that their accumulation and turnover is differentially regulated. Our data suggest that the proteasome may serve different proteolytic processes and that the enzyme may be involved in cell-specific proteolytic events required for cell proliferation and morphogenesis during early Drosophila development.

Large-scale purification of prosomes from calf's liver

Prosomes, cytoplasmatic ribonucleoprotein complexes containing small ribonucleic acid (19S small cytoplasmic RNPs), are ubiquitous in eukaryotic organisms. A new method for the preparation of prosomes in large amounts, starting with ca. 2 kg of calf's liver, is described. A combination of centrifugation and low- and high-pressure chromatography was used to purify intact particles. An alternative purification of prosomes with Solanum tuberosum agglutinin bound to divinyl sulphone-activated agarose is discussed. Calf's liver prosomes have a similar protein composition and RNA content to prosomes isolated from other tissues.

Selection of prosomes and prosomal RNA by immobilized viral RNAs

Viral messengers were used to select and purify prosomes and prosomal RNA from subribosomal fractions of HeLa cells and mouse erythroblasts. Adenovirus mRNA immobilized on oligo(dT)-cellulose and tobacco mosaic virus RNA (TMV) sedimenting in sucrose gradients associated strongly with prosomes at high salt conditions forming intermolecular RNA-RNA hybrids between prosomal RNA and viral RNA. Hybrid selection of small cytoplasmic RNAs with immobilized TMV-RNA revealed a RNA species migrating at the same position as prosomal RNA. The possible existence of a box-like sequence involved in hybridization will be discussed.

The prosomal protein of 27 kDa and a nuclear 38 kDa protein are immunologically related

A monoclonal antibody, recognizing the prosomal 27 kDa protein, was used to detect prosomal proteins in nuclear fractions. Protein gel electrophoresis and immunoblotting revealed large amounts of a 38 kDa protein and in very low amount a 27 kDa protein reacting with the monoclonal antibody. Immunoblot analysis of V8 proteolytic fragments demonstrated that both proteins are intimately related and suggest that the nuclear 38 kDa protein could be a precursor of the 27 kDa protein (pros P 27) which is a structural component of cytoplasmic prosomes.

The Drosophila PROS-28.1 gene is a member of the proteasome gene family

In the present communication, we report the identification of a new gene family which encodes the protein subunits of the proteasome. The proteasome is a high-Mr complex possessing proteolytic activity. Screening a Drosophila lambda gt11 cDNA expression library with the proteasome-specific antibody N19-28 we isolated a clone encoding the 28-kDa No. 1 proteasome protein subunit. In accordance with the nomenclature of proteasome subunits in Drosophila, the corresponding gene is designated PROS-28.1, and it encodes an mRNA of 1.1 kb with an open reading frame of 249 amino acids (aa). Genomic Southern-blot hybridization shows PROS-28.1 to be a member of a family of related genes. Analysis of the predicted aa sequence reveals a potential nuclear targeting signal, a potential site for tyrosine kinase and a potential cAMP/cGMP-dependent phosphorylation site. The aa sequence comparison of the products of PROS-28.1 and PROS-35 with the C2 proteasome subunit of rat shows a strong sequence similarity between the different proteasome subunits. The data suggest that at least a subset of the proteasome-encoding genes belongs to a family of related genes (PROS gene family) which may have evolved from a common ancestral PROS gene.

Prosomes, subcomplexes of untranslated mRNP

PROSOMES are a novel class of small RNP particles of uniform morphology, but of variable RNA (pRNA) and protein composition (about 650,000 MW; 12 nm diameter in the EM). They were discovered as subcomplexes of free mRNP, tightly attached to inactive mRNA in the cytoplasm. The pRNAs hybridize stably to mRNA. Prosomes associate in vitro to mRNA and inhibit cell free protein synthesis inducing an mRNA structure unable to interact with ribosomes. Many types of prosomes were observed. The individual particle is made up by a variable combination of about 20 characteristic proteins and one or several pRNa. Some prosomal proteins are glycosylated, phosphorylated and, possibly, ADP-ribosylated and are highly conserved in evolution whilst others vary with the species and the mRNA population they are associated to. A protease activity was found associated to prosomes. The function(s) of the prosomes is(are) still unknown. The differential inhibition of in vitro protein synthesis points to a capacity to recognize mRNA and to keep it in an inactive state. The observation with the aid of monoclonal antibodies (pMABs) that prosomes and thus mRNP are attached to the intermediate filaments (IF) raises the question if one of the functions of the IF might be in the topological distribution of mRNA within the cell. Similar to the cytokeratin fibers, the prosome networks bridge neighboring cells at specific positions. The nucleus also contains some prosomal antigens, located on chromosomes and on the nuclear matrix. Their presence and distribution in the cell compartments varies with the cell type and the prosomal antigen probed. Oocytes contain large amounts of prosomes.(ABSTRACT TRUNCATED AT 250 WORDS)

Addition of ATP increases the apparent molecular mass of the multicatalytic proteinase, ingensin

A high-molecular mass ATP-dependent proteinase was shown to be identical to a multicatalytic proteinase, ingensin [(1988) Eur. J. Biochem. 177, 261-266]. The molecular mass of this proteinase increased in crude extracts of the rat liver and porcine brain, but not in the purified sample, only when the proteinase was extracted with ATP. The higher-molecular form of ingensin may be the intact one, because the concentration of ATP in vivo never decreases below 1 mM. This form of the proteinase is latent and it requires a high concentration of detergent for activation. On chromatography, it was found that the high-molecular form corresponds to the previously reported minor isoenzyme of ingensin [(1986) Biochim. Biophys. Acta 882, 297-304], ingensin A, or possibly to the ATP/ubiquitin-dependent 26S protease [(1987) J. Biol. Chem. 262, 8303-8313], and the low-molecular form to major ingensin B or the ATP/ubiquitin-independent 20 S protease.

Cytoplasmic heat shock granules are formed from precursor particles and are associated with a specific set of mRNAs

In heat-shocked tomato cell cultures, cytoplasmic heat shock granules (HSGs) are tightly associated with a specific subset of mRNAs coding mainly for the untranslated control proteins. This messenger ribonucleoprotein complex was banded in a CsCl gradient after fixation with formaldehyde (approximately 1.30 g/cm3). It contains all the heat shock proteins and most of the RNA applied to the gradient. During heat shock, a reversible aggregation of HSGs from 15S precursor particles can be shown. These pre-HSGs are not identical to the 19S plant prosomes. Ultrastructural analysis supports the ribonucleoprotein nature of HSGs and their composition of approximately 10-nm precursor particles. A model summarizes our results. It gives a reasonable explanation for the striking conservation of untranslated mRNAs during heat shock and may apply also to animal cells.

Cytoplasmic heat shock granules are formed from precursor particles and are associated with a specific set of mRNAs

In heat-shocked tomato cell cultures, cytoplasmic heat shock granules (HSGs) are tightly associated with a specific subset of mRNAs coding mainly for the untranslated control proteins. This messenger ribonucleoprotein complex was banded in a CsCl gradient after fixation with formaldehyde (approximately 1.30 g/cm3). It contains all the heat shock proteins and most of the RNA applied to the gradient. During heat shock, a reversible aggregation of HSGs from 15S precursor particles can be shown. These pre-HSGs are not identical to the 19S plant prosomes. Ultrastructural analysis supports the ribonucleoprotein nature of HSGs and their composition of approximately 10-nm precursor particles. A model summarizes our results. It gives a reasonable explanation for the striking conservation of untranslated mRNAs during heat shock and may apply also to animal cells.

Evidence for a highly nuclease resistant RNA fragment in prosomes

Prosomes, small cytoplasmic particles of mouse erythroblasts were found to contain low molecular weight RNA molecules in the range of 80 nucleotides. Nuclease digestion of prosomes suggests that prosomal proteins cover and protect almost the whole length of their RNA(s). Our results demonstrate clearly that RNA is an intrinsic component of prosomes.

Virus-ribosome complexes from cell-free translation systems supplemented with cowpea chlorotic mottle virus particles

When particles of cowpea chlorotic mottle virus (CCMV) were added to cell-free extracts from wheat germ, the encapsidated viral genome was translated into polypeptides similar to the translation products specified by unencapsidated viral RNA (as shown before by M.J. Brisco, R. Hull, and T.M.A. Wilson, 1986, Virology 148, 210-217). The rate of protein synthesis observed upon addition of virus particles was much slower than that of extracted RNA and the quantity of protein formed was only 10% of that of extracted RNA. Using sucrose and cesium-chloride gradient analysis, virus-ribosome complexes, containing up to four ribosomes per virus particle, were isolated from translation mixtures supplemented with CCMV particles. These complexes, with densities intermediate of those of virus (1.36 g cm-3) and ribosomes (1.58 g cm-3), were analyzed and quantified in the electron microscope. Less than 5% of the particles was found in association with ribosomes. To verify whether these complexes were involved in the process of cotranslational disassembly, tobacco mosaic virus was analyzed with the same techniques and methods. The results found for TMV were similar to those found for CCMV except that virus-ribosome complexes with up to 20 ribosomes per virus particle were observed. The implications of the process of virion-directed translation for the structure of the particle as well as the role of this process in vivo are discussed.

Intracellular vesicular stomatitis virus nucleocapsids and virions visualized by surface spreading

Spreading of cells on a solution surface could visualize vesicular stomatitis virus nucleocapsids and virions in infected cells easily and clearly without the need for any purification. Characteristic structures observed by the spreading of the infected cells are described and discussed.

Novel virus-like particles containing circular single-stranded DNAs associated with subterranean clover stunt disease

Novel virus-like particles, 17-19 nm in diameter, have been isolated from subterranean clover and pea plants infected with the pathogen of subterranean clover stunt disease (SCSD). The structure and genetic organization of these particles suggest that the pathogen of SCSD is representative of a new group of plant DNA viruses. SCS virus-like particles (SCSV) are isometric and band as a single component with buoyant densities of 1.24 g/ml in Cs2SO4 and 1.34 g/ml in CsCl. The A260 nm/A280 nm is about 1.35, which is consistent with an estimated nucleic acid content of 17%. Molecular calculations suggest that the particles have a T = 1 capsid structure containing 60 polypeptide subunits each with Mr of 19,000. Nucleic acid analysis including restriction enzyme digestions of double-stranded cDNAs suggests that SCSV have a divided genome composed of multiple species of circular, single-stranded DNA molecules each of approximately 850-880 nucleotides and that each is encapsidated in a separate particle. Linear and aggregated forms of these DNAs are also detected by gel electrophoresis. Evidence suggests that these virus-like particles are the pathogen of SCSD.

Prosomes, small cytoplasmic RNP particles, contain glycoproteins

Prosomes, ubiquitous small ribonucleoprotein complexes, were isolated from the cytoplasm of erythropoietic mouse cells induced by Friend leucemia virus. We present evidence that some of the prosomal proteins are glycosylated. Specific reactions with the biotinylated lectins concanavalin agglutinin (Con A), Solanum tuberosum agglutinin (STA) and Limulus polyphemus agglutinin (LPA) indicate that the carbohydrate moieties contain N-acetylneuraminic acid, N-acetylglucosamine and mannosyl- or glucosyl-residues. Glycosylation of prosomal proteins could explain the resistance of prosomes to proteinase K digestion.

The association of prosomes with some of the intermediate filament networks of the animal cell

The small RNP complexes of defined morphology and biochemical composition termed prosomes, first isolated from the cytoplasm associated with repressed mRNA (Martins de Sa, C., M.-F. Grossi de Sa, O. Akhayat, F. Broders, and K. Scherrer. J. Mol. Biol. 1986. 187:47-493), were found also in the nucleus (Grossi de Sa, M.-F., C. Martins de Sa, F. Harper, O. Coux, O. Akhayat, P. Gounon, J. K. Pal, Y. Florentin, and K. Scherrer. 1988. J. Cell Sci. 89:151-165). Immunofluorescence, immunoelectron microscopy, and immunochemical studies using mAbs directed against some of the prosomal proteins of duck erythroblasts indicate that in the cytoplasm of HeLa and PtK cells, prosome antigens are associated with the intermediate filament network of the cytokeratin type.