Proteasome (prosome) associated endonuclease activity

Transcriptome-Wide Identification of Coding and Noncoding RNA-Binding Proteins Defines the Comprehensive RNA Interactome of Leishmania mexicana

Proteomic profiling of RNA-binding proteins in Leishmania is currently limited to polyadenylated mRNA-binding proteins, leaving proteins that interact with nonadenylated RNAs, including noncoding RNAs and pre-mRNAs, unidentified. Using a combination of unbiased orthogonal organic phase separation methodology and tandem mass tag-labeling-based high resolution quantitative proteomic mass spectrometry, we robustly identified 2,417 RNA-binding proteins, including 1289 putative novel non-poly(A)-RNA-binding proteins across the two main Leishmania life cycle stages. Eight out of 20 Leishmania deubiquitinases, including the recently characterized L. mexicana DUB2 with an elaborate RNA-binding protein interactome were exclusively identified in the non-poly(A)-RNA-interactome. Additionally, an increased representation of WD40 repeat domains were observed in the Leishmania non-poly(A)-RNA-interactome, thus uncovering potential involvement of this protein domain in RNA-protein interactions in Leishmania. We also characterize the protein-bound RNAs using RNA-sequencing and show that in addition to protein coding transcripts ncRNAs are also enriched in the protein-RNA interactome. Differential gene expression analysis revealed enrichment of 142 out of 195 total L. mexicana protein kinase genes in the protein-RNA-interactome, suggesting important role of protein-RNA interactions in the regulation of the Leishmania protein kinome. Additionally, we characterize the quantitative changes in RNA-protein interactions in hundreds of Leishmania proteins following inhibition of heat shock protein 90 (Hsp90). Our results show that the Hsp90 inhibition in Leishmania causes widespread disruption of RNA-protein interactions in ribosomal proteins, proteasomal proteins and translation factors in both life cycle stages, suggesting downstream effect of the inhibition on protein synthesis and degradation pathways in Leishmania. This study defines the comprehensive RNA interactome of Leishmania and provides in-depth insight into the widespread involvement of RNA-protein interactions in Leishmania biology. IMPORTANCE Advances in proteomics and mass spectrometry have revealed the mRNA-binding proteins in many eukaryotic organisms, including the protozoan parasites Leishmania spp., the causative agents of leishmaniasis, a major infectious disease in over 90 tropical and subtropical countries. However, in addition to mRNAs, which constitute only 2 to 5% of the total transcripts, many types of non-coding RNAs participate in crucial biological processes. In Leishmania, RNA-binding proteins serve as primary gene regulators. Therefore, transcriptome-wide identification of RNA-binding proteins is necessary for deciphering the distinctive posttranscriptional mechanisms of gene regulation in Leishmania. Using a combination of highly efficient orthogonal organic phase separation method and tandem mass tag-labeling-based quantitative proteomic mass spectrometry, we provide unprecedented comprehensive molecular definition of the total RNA interactome across the two main Leishmania life cycle stages. In addition, we characterize for the first time the quantitative changes in RNA-protein interactions in Leishmania following inhibition of heat shock protein 90, shedding light into hitherto unknown large-scale downstream molecular effect of the protein inhibition in the parasite. This work provides insight into the importance of total RNA-protein interactions in Leishmania, thus significantly expanding our knowledge of the emergence of RNA-protein interactions in Leishmania biology.

Regulation of Endoribonuclease Activity of Alpha-Type Proteasome Subunits in Proerythroleukemia K562 Upon Hemin-Induced Differentiation

The proteasome is the main intracellular proteolytic machine involved in the regulation of numerous cellular processes, including gene expression. In addition to their proteolytic activity, proteasomes also exhibit ATPase/helicase (the 19S particle) and RNAse (the 20S particle) activities, which are regulated by post-translational modifications. In this report we uncovered that several 20S particle subunits: α1 (PSMA6), α2 (PSMA2), α4 (PSMA7), α5 (PSMA5), α6 (PSMA1) and α7 (PSMA3) possess RNAse activity against the p53 mRNA in vitro. Furthermore, we found that the RNAse activity of PSMA1 and PSMA3 was regulated upon hemin-induced differentiation of K562 proerythroleukemia cells. The decrease in RNAse activity of PSMA1 and PSMA3 was paralleled by changes in their status of phosphorylation and ubiquitylation. Collectively, our data support the notion that proteasomal RNAse activity may be functionally important and provide insights into the potential mechanism of p53 repression in erythroleukemia cells by RNAse activity of the 20S α-type subunits.

Hepatic expression of proteasome subunit alpha type-6 is upregulated during viral hepatitis and putatively regulates the expression of ISG15 ubiquitin-like modifier, a proviral host gene in hepatitis C virus infection

The interferon-stimulated gene 15 (ISG15) plays an important role in the pathogenesis of hepatitis C virus (HCV) infection. ISG15-regulated proteins have previously been identified that putatively affect this proviral interaction. The present observational study aimed to elucidate the relation between ISG15 and these host factors during HCV infection. Transcriptomic and proteomic analyses were performed using liver samples of HCV-infected (n = 54) and uninfected (n = 10) or HBV-infected controls (n = 23). Primary human hepatocytes (PHH) were treated with Toll-like receptor ligands, interferons and kinase inhibitors. Expression of ISG15 and proteasome subunit alpha type-6 (PSMA6) was suppressed in subgenomic HCV replicon cell lines using specific siRNAs. Comparison of hepatic expression patterns revealed significantly increased signals for ISG15, IFIT1, HNRNPK and PSMA6 on the protein level as well as ISG15, IFIT1 and PSMA6 on the mRNA level in HCV-infected patients. In contrast to interferon-stimulated genes, PSMA6 expression occurred independent of HCV load and genotype. In PHH, the expression of ISG15 and PSMA6 was distinctly induced by poly(I:C), depending on IRF3 activation or PI3K/AKT signalling, respectively. Suppression of PSMA6 in HCV replicon cells led to significant induction of ISG15 expression, thus combined knock-down of both genes abrogated the antiviral effect induced by the separate suppression of ISG15. These data indicate that hepatic expression of PSMA6, which is upregulated during viral hepatitis, likely depends on TLR3 activation. PSMA6 affects the expression of immunoregulatory ISG15, a proviral factor in the pathogenesis of HCV infection. Therefore, the proteasome might be involved in the enigmatic interaction between ISG15 and HCV.

Stress response factors as hub-regulators of microRNA biogenesis: implication to the diseased heart

MicroRNAs (miRNAs) are important regulators of heart function and then an intriguing therapeutic target for plenty of diseases. The problem raised is that many data in this area are contradictory, thus limiting the use of miRNA-based therapy. The goal of this review is to describe the hub-mechanisms regulating the biogenesis and function of miRNAs, which could help in clarifying some contradictions in the miRNA world. With this scope, we analyse an array of factors, including several known agents of stress response, mediators of epigenetic changes, regulators of alternative splicing, RNA editing, protein synthesis and folding and proteolytic systems. All these factors are important in cardiovascular function and most of them regulate miRNA biogenesis, but their influence on miRNAs was shown for non-cardiac cells or some specific cardiac pathologies. Finally, we consider that studying the stress response factors, which are upstream regulators of miRNA biogenesis, in the diseased heart could help in (1) explaining some contradictions concerning miRNAs in heart pathology, (2) making the role of miRNAs in pathogenesis of cardiovascular disease more clear, and therefore, (3) getting powerful targets for its molecular therapy.

DNA damage modulates interactions between microRNAs and the 26S proteasome

26S proteasomes are known as major non-lysosomal cellular machines for coordinated and specific destruction of ubiquitinylated proteins. The proteolytic activities of proteasomes are controlled by various post-translational modifications in response to environmental cues, including DNA damage. Besides proteolysis, proteasomes also associate with RNA hydrolysis and splicing. Here, we extend the functional diversity of proteasomes by showing that they also dynamically associate with microRNAs (miRNAs) both in the nucleus and cytoplasm of cells. Moreover, DNA damage induced by an anti-cancer drug, doxorubicin, alters the repertoire of proteasome-associated miRNAs, enriching the population of miRNAs that target cell cycle checkpoint regulators and DNA repair proteins. Collectively, these data uncover yet another potential mode of action for proteasomes in the cell via their dynamic association with microRNAs.

Does proteasome regulate the level of microRNA-1 in cardiomyocytes? Application to anoxia-reoxygenation

Proteasome and microRNAs play a critical role in almost all processes in a living organism, including pathology of the heart; however, their interaction is still in question. In the present study, we have found that proteasome inhibitor provoked increase of mature but not immature microRNA-1 in cultured cardiomyocytes, and tested the hypothesis that mature microRNA-1 can be a substrate for endonuclease activity of proteasome. In our in vitro experiments, we have found that proteasome fraction II is able to degrade both mature and primary but not precursor microRNA-1. However, this in vitro effect was not abolished by chemical inhibitor of proteolytic activities of proteasome. These data let us summarize that proteasome has the complex effect on the level of microRNA-1.

Functional interactions between mRNA turnover and surveillance and the ubiquitin proteasome system

The proteasome is a critical regulator of protein levels within the cell and is essential for maintaining homeostasis. A functional proteasome is required for effective mRNA surveillance and turnover. During transcription, the proteasome localizes to sites of DNA breaks, degrading RNA polymerase II and terminating transcription. For fully transcribed and processed messages, cytoplasmic surveillance is initiated with the pioneer round of translation. The proteasome is recruited to messages bearing premature termination codons, which trigger nonsense-mediated decay (NMD), as well as messages lacking a termination codon, which trigger nonstop decay, to degrade the aberrant protein produced from these messages. A number of proteins involved in mRNA translation are regulated in part by proteasome-mediated decay, including the initiation factors eIF4G, eIF4E, and eIF3a, and the poly(A)-binding protein (PABP) interacting protein, Paip2. eIF4E-BP (4E-BP) is differentially regulated by the proteasome: truncated to generate a protein with higher eIF4B binding or completely degraded, depending on its phosphorylation status. Finally, a functional proteasome is required for AU-rich-element (ARE)-mediated decay but the specific role the proteasome plays is unclear. There is data indicating the proteasome can bind to AREs, act as an endonuclease, and degrade ARE-binding proteins. How these events interact with the 5'-to-3' and 3'-to-5' decay pathways is unclear at this time; however, data is provided indicating that proteasomes colocalize with Xrn1 and the exosome RNases Rrp44 and Rrp6 in untreated HeLa cells.

Cytoskeleton-associated large RNP complexes in tobacco male gametophyte (EPPs) are associated with ribosomes and are involved in protein synthesis, processing, and localization

The progamic phase of male gametophyte development involves activation of synthetic and catabolic processes required for the rapid growth of the pollen tube. It is well-established that both transcription and translation play an important role in global and specific gene expression patterns during pollen maturation. On the contrary, germination of many pollen species has been shown to be largely independent of transcription but vitally dependent on translation of stored mRNAs. Here, we report the first structural and proteomic data about large ribonucleoprotein particles (EPPs) in tobacco male gametophyte. These complexes are formed in immature pollen where they contain translationally silent mRNAs. Although massively activated at the early progamic phase, they also serve as a long-term storage of mRNA transported along with the translational machinery to the tip region. Moreover, EPPs were shown to contain ribosomal subunits, rRNAs and a set of mRNAs. Presented results extend our view of EPP complexes from mere RNA storage and transport compartment in particular stages of pollen development to the complex and well-organized machinery devoted to mRNA storage, transport and subsequent controlled activation resulting in protein synthesis, processing and precise localization. Such an organization is extremely useful in fast tip-growing pollen tube. There, massive and orchestrated protein synthesis, processing, and transport must take place in accurately localized regions. Moreover, presented complex role of EPPs in tobacco cytoplasmic mRNA and protein metabolism makes them likely to be active in another plant species too. Expression of vast majority of the closest orthologues of EPP proteins also in Arabidopsis male gametophyte further extends this concept from tobacco to Arabidopsis, the model species with advanced tricellular pollen.

Role of proteasomes in cellular regulation

The 26S proteasome is the key enzyme of the ubiquitin-dependent pathway of protein degradation. This energy-dependent nanomachine is composed of a 20S catalytic core and associated regulatory complexes. The eukaryotic 20S proteasomes demonstrate besides several kinds of peptidase activities, the endoribonuclease, protein-chaperone and DNA-helicase activities. Ubiquitin-proteasome pathway controls the levels of the key regulatory proteins in the cell and thus is essential for life and is involved in regulation of crucial cellular processes. Proteasome population in the cell is structurally and functionally heterogeneous. These complexes are subjected to tightly organized regulation, particularly, to a variety of posttranslational modifications. In this review we will summarize the current state of knowledge regarding proteasome participation in the control of cell cycle, apoptosis, differentiation, modulation of immune responses, reprogramming of these particles during these processes, their heterogeneity and involvement in the main levels of gene expression.

Potyviral NIa proteinase, a proteinase with novel deoxyribonuclease activity

The NIa proteinase from pepper vein banding virus (PVBV) is a sequence-specific proteinase required for processing of viral polyprotein in the cytoplasm. It accumulates in the nucleus of the infected plant cell and forms inclusion bodies. The function of this protein in the nucleus is not clear. The purified recombinant NIa proteinase was active, and the mutation of the catalytic residues His-46, Asp-81, and Cys-151 resulted in complete loss of activity. Most interesting, the PVBV NIa proteinase exhibited previously unidentified activity, namely nonspecific double-stranded DNA degradation. This DNase activity of the NIa proteinase showed an absolute requirement for Mg(2+). Site-specific mutational analysis showed that of the three catalytic residues, Asp-81 was the crucial residue for DNase activity. Mutation of His-46 and Cys-151 had no effect on the DNase activity, whereas mutant D81N was partially active, and D81G was completely inactive. Based on kinetic analysis and molecular modeling, a metal ion-dependent catalysis similar to that observed in other nonspecific DNases is proposed. Similar results were obtained with glutathione S-transferase-fused PVBV NIa proteinase and tobacco etch virus NIa proteinase, confirming that the DNase function is an intrinsic property of potyviral NIa proteinase. The NIa protein present in the infected plant nuclear extract also showed the proteinase and the DNase activities, suggesting that the PVBV NIa protein that accumulates in the nucleus late in the infection cycle might serve to degrade the host DNA. Thus the dual function of the NIa proteinase could play an important role in the life cycle of the virus.

cis-Inhibition of proteasomal degradation by viral repeats: impact of length and amino acid composition

The Gly-Ala repeat (GAr) of the Epstein-Barr virus nuclear antigen 1 is a cis acting inhibitor of ubiquitin-proteasome proteolysis. We have investigated the capacity of various repeats to inhibit the turnover of the proteasomal substrate IkappaBalpha. Inhibition of TNFalpha-induced degradation was achieved by insertion of octamers containing three alanines or valines, interspersed by no more then three consecutive glycines. The inhibitory activity was abolished by increasing the length of the spacer, by eliminating the spacers, or by substitution of a single hydrophobic residue with a polar or charged residue. A serine containing octamer was inactive but inhibition was partially restored by insertion of three consecutive repeats. These findings suggest a model where inhibition requires the interaction of at least three alanine residues of the GAr in a beta-strand conformation with adjacent hydrophobic binding pockets of a putative receptor.

Prosomes form sarcomere-like banding patterns in skeletal, cardiac, and smooth muscle cells

Prosomes (20S proteasomes) constitute the catalytic core of the 26S proteasomes, but were first observed as factors associated with unstranslated mRNA. Recently, their RNase activity was discovered together with the fact that their proteolytic function is dispensable in adapted human cells. By indirect immunofluorescence using monoclonal antibodies, we demonstrate as a general phenomenon, regular intercalation of specific types of prosomes into the sarcomeric structure of all types of striated muscle. Surprisingly, in cultured smooth muscle cells without sarcomeric organization, some prosomes also form regular striations in extended projections of cytoplasmic regions. The significance of their sarcomeric distribution is not understood as yet, but the pattern we observe is very similar to that shown by others for muscle-specific mRNAs, identified by in situ hybridization, and that of the cognate proteins. A role of prosomes in the cotranslational assembly of the myofibrillar proteins is suggested, since prosomes organize into pseudo-sarcomeric patterns prior to formation de novo of the actin-myosin arrangement.

In mouse myoblasts nuclear prosomes are associated with the nuclear matrix and accumulate preferentially in the perinucleolar areas

Prosomes are the core of 26S proteasomes, although they were originally observed as 20S particles associated with cytoplasmic mRNPs. Here we show for the first time that prosomes are also genuine constituents of the nuclear matrix, chromatin and the nuclear RNP networks. Using mouse myoblasts we tested three monoclonal antibodies recognising the prosomal subunits p23K, p27K and p30K, and found that the corresponding prosome subclasses are characterised by a variable distribution pattern within the nuclei. Their presence on the nuclear matrix, and most abundantly in the perinucleolar area, is of particular importance. When myoblasts fuse into myotubes, the distribution pattern of certain types of prosomes on the nuclear matrix changes drastically. Surprisingly, DNA strongly interferes with the detection of prosomal antigens by immunofluorescence methods, whereas RNA, histones and other proteins soluble in 2 M NaCl have no such effect. This ‘masking’ of prosomes can be completely overcome by extensive or even mild digestion with DNase I or restriction enzymes. Many nuclear prosomes can be solubilized by combined treatment with 0.5% Triton X-100 and 2 M NaCl, and others can be released by digestion of DNA and/or RNA, and about 10–20% of nuclear prosomes remain tightly bound to the protein-based nuclear matrix.

Specific types of prosomes distribute differentially between intermediate and actin filaments in epithelial, fibroblastic and muscle cells

First observed as components of non-translated mRNP complexes, prosomes harbour RNase and several proteinase activities; they are also the central constituent of the "Multicatalytic Proteinase (MCP) complexes" or "26S-proteasomes". In two recent publications (Arcangeletti et al., 1997b; De Conto et al., 1997) we have shown, by applying a new fixation technique, that these particles distribute differentially between the cytoskeletal networks of intermediate filament (IF) and actin types; previously they had been observed exclusively on the intermediate filaments. Here we further investigate the distribution of prosomes of several types, distinct by their subunit composition, between the IF of vimentin type and the actin network, as well as in the 3D space of the cell. It is shown that subtypes of prosomes occupy specific networks of the cytoskeleton, and that this pattern is specific for a given cell type. Confocal microscopy shows that prosome cytodistribution is not homogeneous in the 3D space: in the perinuclear area they colocalize most strongly with the IF, and more peripherally with the microfilament/stress fiber system; connections may exist between the two networks. Furthermore, new data indicate that the prosome-actin interaction may participate in the molecular structure of the stress fibers.

The specific endoribonuclease activity of small nuclear and cytoplasmic alpha-RNPs

For the first time small nuclear ribonucleoprotein particles (alpha-RNP) tightly bound to chromatin as well as cytoplasmic alpha-RNP are shown to possess strong and regulated endonuclease activity specific for mRNAs and hnRNAs. The enzymatic nature of this activity is confirmed, and the optimal conditions detected. This RNase activity is controlled by the action of a differentiating stimulus, dimethylsulfoxide, in human K562 cells. Small alpha-RNP involvement in the coordinated control of stability of pre-messenger RNA and messenger RNA molecules is suggested.

In the nucleus and cytoplasm of chicken erythroleukemic cells, prosomes containing the p23K subunit are found in centers of globin (pre-)mRNA processing and accumulation

Prosomes were originally identified as 20S particles associated with untranslated mRNA; they also constitute the core of the 26S proteasomes. The cellular distribution of three types of prosomes characterized by the presence of subunits with molecular masses of 23, 27, and 30 kDa was analyzed using an immunocytochemical approach on cultured chicken erythroblasts. The prosomes containing the p27K and p30K subunits were found in diffuse distribution in both nuclei and cytoplasm. In contrast, the prosomes containing the p23K subunit, although relatively rare in the nuclear space, were found concentrated in one or two large spots. Using in situ hybridization with an alpha(A)-globin gene-specific riboprobe we found that the p23K-type prosomes colocalize in the nucleus with centers of globin (pre-)mRNA processing, and of mRNA accumulation in the cytoplasm. This result suggests there is local coincidence of specific-type prosome function with processing and, possibly, transport of a particular kind of (pre-)mRNA.

Relationships between proteasomes and viral gene products

The interrelationships between proteasomes and viral gene products are very complex. 20S proteasomes associate with a number of viral mRNAs which are cleaved by proteasome's associated endonuclease activity. In addition proteasome's endopeptidase activities are involved in the presentation of viral antigens. Viral proteins of different origin associate with the 20S and 26S complexes and interfere with their enzymatic activities. A major part of this review deals with the interactions between 20S proteasomes and the gene products of the human immunodeficiency virus (HIV) which has been studied in detail by our group.

Proteasome subunit zeta, a putative ribonuclease, is also found as a free monomer

20 S Proteasomes are large proteinase complexes found in eukaryotic cells where they degrade cell proteins in an ATP-dependent manner. Proteasomes consist of 14 different subunits. One of them, zeta, was found in HeLa cells at a concentration of 890 microg per g of cell protein. A large proportion of zeta was found in the free state rather than incorporated into proteasomes, namely 28% in HeLa cells and 37% in BSC-1 cells. Free zeta was found in both nuclei and cytoplasm. In HeLa cells free zeta had a t1/2 of 2.8 h, compared to 5 d for proteasomes, and did not exchange with zeta in proteasomes. We confirmed (Petit F et al.: Biochem. J. 326: 93-98 (1997)) that both 20 S proteasomes and free zeta subunits possess RNase activity though the activities were very low: 4 mMoles and 0.6 mMoles of tobacco mosaic virus RNA degraded per mole of enzyme per min, respectively. The physiological function of the relatively abundant zeta monomers is not known.

Dynamic distribution and formation of a para-sarcomeric banding pattern of prosomes during myogenic differentiation of satellite cells in vitro

Myogenesis proceeds by fusion of proliferating myoblasts into myotubes under the control of various transcription factors. In adult skeletal muscle, myogenic stem cells are represented by the satellite cells which can be cultured and differentiate in vitro. This system was used to investigate the subcellular distribution of a particular type of prosomes at different steps of the myogenic process. Prosomes constitute the MCP core of the 26S proteasomes but were first observed as subcomplexes of the untranslated mRNPs; recently, their RNase activity was discovered. A monoclonal antibody raised against the p27K subunit showed that the p27K subunit-specific prosomes move transiently into the nucleus prior to the onset of myoblast fusion into myotubes; this represents possibly one of the first signs of myoblast switching into the differentiation pathway. Prior to fusion, the prosomes containing the p27K subunit return to the cytoplasm, where they align with the gradually formed lengthwise-running desmin-type intermediate filaments and the microfilaments, co-localizing finally with the actin bundles. The prosomes progressively form discontinuous punctate structures which eventually develop a pseudo-sarcomeric banding pattern. In myotubes just formed in vitro, the formation of this pattern seems to preceed that produced by the muscle-specific sarcomeric (alpha)-actin. Interestingly, this pattern of prosomes of myotubes in terminal in vitro differentiation was very similar to that of prosomes observed in vivo in foetal and adult muscle. These observations are discussed in relation to molecular myogenesis and prosome/proteasome function.

Possible involvement of proteasomes (prosomes) in AUUUA-mediated mRNA decay

We have identified a cellular target for proteasomal endonuclease activity. Thus, 20 S proteasomes interact with the 3'-untranslated region of certain cytoplasmic mRNAs in vivo, and 20 S proteasomes isolated from Friend leukemia virus-infected mouse spleen cells were found to be associated with a mRNA fragment showing great homology to the 3'-untranslated region of tumor necrosis factor-beta mRNA that contains AUUUA sequences. We furthermore demonstrate that 20 S proteasomes destabilize oligoribonucleotides corresponding to the 3'-untranslated region of tumor necrosis factor-alpha, creating a specific cleavage pattern. The cleavage reaction is accelerated with increasing number of AUUUA motifs, and major cleavage sites are localized at the 5' side of the A residues. These results strongly suggest that 20 S proteasomes could be involved in the destabilization of cytokine mRNAs such as tumor necrosis factor mRNAs and other short-lived mRNAs containing AUUUA sequences.