Tubacin Kills Epstein-Barr Virus (EBV)-Burkitt Lymphoma Cells by Inducing Reactive Oxygen Species and EBV Lymphoblastoid Cells by Inducing Apoptosis

Tubacin is a small molecule inhibitor of histone deacetylase 6 and blocks aggresome activity. We found that Epstein-Barr virus (EBV)-positive Burkitt lymphoma (BL) cells were generally killed by lower doses of tubacin than EBV-transformed lymphoblastoid cells (LCLs) or EBV-negative BL cells. Tubacin induced apoptosis of LCLs, which was inhibited by pretreatment with a pancaspase inhibitor but not by butylated hydroxyanisole, which inhibits reactive oxygen species. In contrast, tubacin killed EBV-positive BL cells in a caspase-3-independent pathway that involved reactive oxygen species and was blocked by butylated hydroxyanisole. Previously, we showed that bortezomib, a proteasome inhibitor, induces apoptosis of EBV LCLs and that LCLs are killed by lower doses of bortezomib than EBV-positive BL cells. Here we found that the combination of bortezomib and tubacin acted in synergy to kill EBV-positive BL cells and LCLs. Tubacin or the combination of bortezomib and tubacin did not induce EBV lytic replication. These findings suggest that the combination of a proteasome inhibitor and an HDAC6 inhibitor may represent a useful strategy for the treatment of certain EBV-associated B cell lymphomas.Epstein-Barr virus (EBV)⁴ is associated with several human lymphoid malignancies, including Hodgkin disease, Burkitt lymphoma (BL), T cell lymphomas, and post-transplant lymphoproliferative disease (1, 2). Tissues from patients with EBV post-transplant lymphoproliferative disease typically have a type 3 latency pattern in which each of the EBV latency-associated proteins, including EBV nuclear antigens (EBNA-1, -2, -3A, -3B, and -3C) and latent membrane proteins (LMP1 and LMP2) are expressed. A type 3 latency pattern is also seen in lymphoblastoid cell lines (LCLs), derived from primary B cells transformed with EBV in vitro. Tissues from patients with EBV-positive BL usually have a type 1 latency pattern with expression of EBNA-1 but not the other latency-associated proteins. When grown in cell culture, BL cell lines can have a type 1 or a type 3 pattern of latency.The treatment of EBV-associated lymphoid malignancies often requires cytotoxic chemotherapy, which is not always successful. Inhibition of proteasomes and aggresomes represents new therapeutic targets for malignancies (3–5). Degradation of proteins is required for vital cell functions and is carried out both in proteasomes and aggresomes. Misfolded or unfolded proteins are polyubiquitinated by a complex of proteins and subsequently degraded by proteasomes. However, if ubiquitinated proteins escape degradation by proteasomes and aggregate, they accumulate into aggresomes (6). Aggresome formation can be abrogated by disrupting the microtubule cytoskeleton or by overexpression of the p50 subunit of dynactin (7). HDAC6 (histone deacetylase 6) is a microtubule-associated deacetylase that can induce microtubule disassembly and promote chemotactic cell motility (8–10). HDAC6 contains a dynein motor binding domain, two catalytic domains with histone deacetylase activity, and a carboxyl-terminal domain that binds polyubiquitinated misfolded proteins (11). The carboxyl catalytic domain of HDAC6 possesses α-tubulin deacetylase activity (12). HDAC6 is required for transport of misfolded proteins for aggresome formation and to prevent apoptosis in response to misfolded protein stress (11). HDAC6 inhibitors disrupt aggresomes (5). Tubacin inhibits the carboxyl catalytic domain of HDAC6, increases the level of acetylated α-tubulin, and blocks aggresome activity (4, 12, 13).Bortezomib is an inhibitor of the 26 S proteasome (3). Previously, we showed that bortezomib induces apoptosis of EBV-transformed B cells and prolongs survival of mice inoculated with EBV-transformed B cells (14). In contrast, EBV-negative Burkitt lymphoma cells were much less sensitive to killing by bortezomib. Since bortezomib has been shown to interact synergistically with tubacin to induce apoptosis in multiple myeloma cells (4), we studied the effect of tubacin on EBV-transformed B cells and Burkitt lymphoma cells both in the absence and presence of bortezomib. We show that tubacin kills LCLs by apoptosis and induction of caspase-3, whereas tubacin kills EBV-positive BL cells by induction of reactive oxygen species. Bortezomib and tubacin acted in synergy to kill EBV-positive BL cells and LCLs. These findings suggest that the combination of tubacin and bortezomib may have potential as a model for the treatment of certain EBV-associated lymphomas.     

Epstein-Barr Virus Lacking Glycoprotein gp42 Can Bind to B Cells but Is Not Able To Infect

The Epstein-Barr virus gH-gL complex includes a third glycoprotein, gp42, which is the product of the BZLF2 open reading frame (ORF). gp42 has been implicated as critical to infection of the B lymphocyte by virtue of its interaction with HLA class II on the B-cell surface. A neutralizing antibody that reacts with gp42 inhibits virus-cell fusion and blocks binding of gp42 to HLA class II; antibody to HLA class II can inhibit infection, and B cells that lack HLA class II can only be infected if HLA class II expression is restored. To confirm whether gp42 is an essential component of the virion, we derived a recombinant virus with a selectable marker inserted into the BZLF2 ORF to interrupt expression of the protein. A complex of gH and gL was expressed by the recombinant virus in the absence of gp42. Recombinant virus egressed from the cell normally and could bind to receptor-positive cells. It had, however, lost the ability to infect or transform B lymphocytes. Treatment with polyethylene glycol restored the infectivity of recombinant virus, confirming that gp42 is essential for penetration of the B-cell membrane.Entry of enveloped viruses into mammalian cells requires that the virion envelope fuse with the cell membrane after attachment to the cell surface. Herpesviruses require the functions of multiple protein species to mediate this event, and in keeping with the common origin and diverse habitats of these viruses, some of the proteins involved in penetration appear to be conserved throughout the family and some appear to be restricted to individual members or more closely related members with similar tropism. The two glycoproteins gH and gL fall into the first category of conserved proteins. Glycoprotein gH has been implicated as a major player in virus-cell fusion in many herpesviruses (8, 10, 11, 22, 28, 32, 34), and gL is an essential partner which is required for folding and transport of gH out of the endoplasmic reticulum (6, 19, 21, 27, 28, 35, 38, 45). The gH and gL homologs of Epstein-Barr virus (EBV) are gp85, the product of the BXLF2 open reading frame (ORF) (13, 31), and gp25, the product of the BKRF2 ORF (45), and these homologs appear to behave much as their counterparts in other herpesviruses do (45). However, a third glycoprotein, gp42, associates with the EBV gH-gL complex and falls into the second category of proteins, those with a more restricted distribution.Glycoprotein gp42 is the product of the BZLF2 ORF (26), and although there may be a functionally similar protein in cytomegalovirus (18, 24), it is not predicted to have a homolog in other human herpesviruses. It does, however, have a homolog in ORF51 of equine herpes virus 2 (43). Both EBV and equine herpes virus 2 infect B lymphocytes (1), and several lines of evidence suggest that, at least in the case of EBV, gp42 is critical to the infection of this cell type. A monoclonal antibody (MAb) called F-2-1 that reacts with gp42 has no affect on EBV attachment to its receptor, complement receptor type 2 (CR2) (CD21), but inhibits fusion of the virus with the B-cell membrane and neutralizes infection (29). Glycoprotein gp42 interacts with the β₁ domain of the HLA class II protein HLA-DR (39), and MAb F-2-1 interferes with this interaction (25). Like F-2-1, a MAb to HLA-DR or a soluble form of gp42 can block B-cell transformation, and B-cell lines which lack expression of HLA class II are not susceptible to superinfection with EBV unless expression of HLA class II is restored (25). Collectively these observations suggest that gp42, probably by virtue of its interaction with HLA class II, is essential to infection of the B lymphocyte. To answer directly the question of whether gp42 is an indispensable glycoprotein, we derived a virus that could be definitively shown to lack expression of the molecule and examined its ability to infect normal resting B lymphocytes. We report here that virus with expression of gp42 blocked can exit cells normally and can bind to receptor-positive target cells. However, it is unable to penetrate into cells and initiate infection.     

Epstein-Barr Virus Uses Different Complexes of Glycoproteins gH and gL To Infect B Lymphocytes and Epithelial Cells

The Epstein-Barr virus (EBV) gH-gL complex includes a third glycoprotein, gp42. gp42 binds to HLA class II on the surfaces of B lymphocytes, and this interaction is essential for infection of the B cell. We report here that, in contrast, gp42 is dispensable for infection of epithelial cell line SVKCR2. A soluble form of gp42, gp42.Fc, can, however, inhibit infection of both cell types. Soluble gp42 can interact with EBV gH and gL and can rescue the ability of virus lacking gp42 to transform B cells, suggesting that a gH-gL-gp42.Fc complex can be formed by extrinsic addition of the soluble protein. Truncated forms of gp42.Fc that retain the ability to bind HLA class II but that cannot interact with gH and gL still inhibit B-cell infection by wild-type virus but cannot inhibit infection of SVKCR2 cells or rescue the ability of recombinant gp42-negative virus to transform B cells. An analysis of wild-type virions indicates the presence of more gH and gL than gp42. To explain these results, we describe a model in which wild-type EBV virions are proposed to contain two types of gH-gL complexes, one that includes gp42 and one that does not. We further propose that these two forms of the complex have mutually exclusive abilities to mediate the infection of B cells and epithelial cells. Conversion of one to the other concurrently alters the ability of virus to infect each cell type. The model also suggests that epithelial cells may express a molecule that serves the same cofactor function for this cell type as HLA class II does for B cells and that the gH-gL complex interacts directly with this putative epithelial cofactor.All herpesviruses examined to date encode a complex of two glycoproteins, gH and gL, that appear to be necessary, if not sufficient, for virus penetration. Glycoprotein gH is generally thought to be the major player in virus cell fusion (5, 6, 8, 14, 20, 25, 26), while the role of gL is to serve as a chaperone, essential for folding and transport of functional gH (3, 11, 13, 20, 21, 28, 29). The Epstein-Barr virus (EBV) gH-gL complex follows this pattern. Glycoprotein gp85, the gH homolog, is retained in the endoplasmic reticulum in the absence of gp25, the EBV gL (38), and virosomes made from EBV proteins depleted of the gH-gL complex bind to cells but fail to fuse (9). The EBV gH-gL complex, however, includes a third glycoprotein, gp42, which is the product of the BZLF2 open reading frame (ORF) (18). This third component has also proven to be essential for penetration of the major target cell of EBV, the B lymphocyte. Several lines of evidence indicate that gp42 is a ligand for HLA class II and, further, that HLA class II functions as a cell surface cofactor for EBV entry into this cell type. Glycoprotein gp42 interacts with the β₁ domain of HLA class II protein HLA-DR (30), and a monoclonal antibody (MAb) to gp42 called F-2-1 interferes with this interaction (17). MAb F-2-1 has no effect on EBV attachment via glycoprotein gp350/220 to its primary receptor, complement receptor type 2 (CR2; CD21) but inhibits the fusion of the virus with the B-cell membrane (22). Similarly, a MAb to HLA-DR or a soluble form of gp42 blocks B-cell transformation. Finally, B-cell lines which lack expression of HLA class II are not susceptible to superinfection with EBV unless expression of class II is restored (17). Most recently, we derived a recombinant virus with gp42 expression deleted and confirmed that loss of the glycoprotein resulted in a virus that attached to the B-cell surface but that failed to penetrate unless it was treated with the fusogenic agent polyethylene glycol (36).Although most is known about the early interactions of EBV with B lymphocytes in vitro since these cells are readily available and easy to culture, infection is not restricted to this cell type in vivo. During our initial analysis of the biology of gp42 we had therefore examined its potential role in infection of a then newly derived model epithelial cell line, SVKCR2. SVKCR2 cells are transformed with simian virus 40 and stably transfected with B-cell receptor CR2 (19). They are poorly infectable with many strains of EBV, but in excess of 30% of the cells can be infected with the Akata strain of virus as judged by the expression of EBV latent protein EBNA 1 (18, 19). We found that MAb F-2-1 had no effect on the infection of SVKCR2 cells. At the same time, a second MAb, E1D1, which reacts with an epitope that can be formed by the coexpression of gH and gL in the absence of gp42, neutralized infection of SVKCR2 cells, but had no effect on the infection of lymphocytes. These data strongly suggested that the involvement of the gH-gL complex in the internalization of virus into the two cell types was different. We hypothesized that just as EBV has evolved a glycoprotein, gp350/220, which is uniquely adapted for attachment to B lymphocytes, so it has evolved a second glycoprotein, gp42, uniquely adapted for penetration into the same cell type (18). The implication was that gp42 might be dispensable for infection of epithelial cells.Since we made our initial observations with SVKCR2 cells, several novel reagents, including the Akata strain virus with the expression of gp42 deleted, have become available. The recent insights into the role of HLA class II in B-cell infection also provided new impetus to reexamine the involvement of the gH-gL complex in epithelial cell infection. We report here that gp42 is not required for infection of SVKCR2 cells despite the fact that the soluble form of the protein that inhibits B-cell infection can also neutralize infection of SVKCR2 cells. To explain these apparently anomalous results, we describe a model which proposes that wild-type EBV virions contain two types of gH-gL complexes, one that includes gp42 and one that does not. We further propose that the tripartite “B-cell complexes” are not functional for infection of epithelial cells, just as the bipartite “epithelial cell complexes” are unable to mediate infection of the B lymphocyte.     

Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome Proceeds Via High Specificity

Comprehensive analysis of the complex nature of the Human Leukocyte Antigen (HLA) class II ligandome is of utmost importance to understand the basis for CD4⁺ T cell mediated immunity and tolerance. Here, we implemented important improvements in the analysis of the repertoire of HLA-DR-presented peptides, using hybrid mass spectrometry-based peptide fragmentation techniques on a ligandome sample isolated from matured human monocyte-derived dendritic cells (DC). The reported data set constitutes nearly 14 thousand unique high-confident peptides, i.e. the largest single inventory of human DC derived HLA-DR ligands to date. From a technical viewpoint the most prominent finding is that no single peptide fragmentation technique could elucidate the majority of HLA-DR ligands, because of the wide range of physical chemical properties displayed by the HLA-DR ligandome. Our in-depth profiling allowed us to reveal a strikingly poor correlation between the source proteins identified in the HLA class II ligandome and the DC cellular proteome. Important selective sieving from the sampled proteome to the ligandome was evidenced by specificity in the sequences of the core regions both at their N- and C- termini, hence not only reflecting binding motifs but also dominant protease activity associated to the endolysosomal compartments. Moreover, we demonstrate that the HLA-DR ligandome reflects a surface representation of cell-compartments specific for biological events linked to the maturation of monocytes into antigen presenting cells. Our results present new perspectives into the complex nature of the HLA class II system and will aid future immunological studies in characterizing the full breadth of potential CD4⁺ T cell epitopes relevant in health and disease.Human Leukocyte Antigen (HLA)¹ class II molecules on professional antigen presenting cells such as dendritic cells (DC) expose peptide fragments derived from exogenous and endogenous proteins to be screened by CD4⁺ T cells (1, 2). The activation and recruitment of CD4⁺ T cells recognizing disease-related peptide antigens is critical for the development of efficient antipathogen or antitumor immunity. Furthermore, the presentation of self-peptides and their interaction with CD4⁺ T cells is essential to maintain immunological tolerance and homeostasis (3). Knowledge of the nature of HLA class II-presented peptides on DC is of great importance to understand the rules of antigen processing and peptide binding motifs (4), whereas the identity of disease-related antigens may provide new knowledge on immunogenicity and leads for the development of vaccines and immunotherapy (5, 6).Mass spectrometry (MS) has proven effective for the analysis HLA class II-presented peptides (4, 7, 8). MS-based ligandome studies have demonstrated that HLA class II molecules predominantly present peptides derived from exogenous proteins that entered the cells by endocytosis and endogenous proteins that are associated with the endo-lysosomal compartments (4). Yet proteins residing in the cytosol, nucleus or mitochondria can also be presented by HLA class II molecules, primarily through autophagy (9–11). Multiple studies have mapped the HLA class II ligandome of antigen presenting cells in the context of infectious pathogens (12), autoimmune diseases (13–17) or cancer (14, 18, 19), or those that are essential for self-tolerance in the human thymus (3, 20). Notwithstanding these efforts, and certainly not in line with the extensive knowledge on the HLA class I ligandome (21), the nature of the HLA class II-presented peptide repertoire and particular its relationship to the cellular source proteome remains poorly understood.To advance our knowledge on the HLA-DR ligandome on activated DC without having to deal with limitations in cell yield from peripheral human blood (12, 21, 22) or tissue isolates (3), we explored the use of MUTZ-3 cells. This cell line has been used as a model of human monocyte-derived DCs. MUTZ-3 cells can be matured to act as antigen presenting cells and express then high levels of HLA class II molecules, and can be propagated in vitro to large cell densities (23–25). We also evaluated the performance of complementary and hybrid MS fragmentation techniques electron-transfer dissociation (ETD), electron-transfer/higher-energy collision dissociation (EThcD) (26), and higher-energy collision dissociation (HCD) to sequence and identify the HLA class II ligandome. Together this workflow allowed for the identification of an unprecedented large set of about 14 thousand unique peptide sequences presented by DC derived HLA-DR molecules, providing an in-depth view of the complexity of the HLA class II ligandome, revealing underlying features of antigen processing and surface-presentation to CD4⁺ T cells.     

Multiple,Non-conserved,Internal Viral Ligands Naturally Presented by HLA-B27 in Human Respiratory Syncytial Virus-infected Cells

Cytotoxic T lymphocyte (CTL)-mediated death of virus-infected cells requires prior recognition of short viral peptide antigens that are presented by human leukocyte antigen (HLA) class I molecules on the surface of infected cells. The CTL response is critical for the clearance of human respiratory syncytial virus (HRSV) infection. Using mass spectrometry analysis of complex HLA-bound peptide pools isolated from large amounts of HRSV-infected cells, we identified nine naturally processed HLA-B27 ligands. The isolated peptides are derived from six internal, not envelope, proteins of the infective virus. The sequences of most of these ligands are not conserved between different HRSV strains, suggesting a mechanism to explain recurrent infection with virus of different HRSV antigenic subgroups. In addition, these nine ligands represent a significant fraction of the proteome of this virus, which is monitored by the same HLA class I allele. These data have implications for vaccine development as well as for analysis of the CTL response.The recognition of short viral peptides associated with human histocompatibility complex (human leukocyte antigen (HLA)¹) class I molecules on the cell surface allows cytotoxic T lymphocytes (CTLs) to recognize and kill virus-infected cells (1). These peptides are generated by proteolytic processing of newly synthesized viral proteins in the cytosol by the combined action of proteasomes, ERAAP (endoplasmic reticulum aminopeptidase associated with antigen processing), and in some cases other peptidases (2). This degradation of viral proteins generates peptides of 8–11 residues that are translocated to the endoplasmic reticulum lumen by transporters associated with antigen processing. These short peptides then assemble with the HLA class I heavy chain and β₂-microglobulin. Usually, two major anchor residues in the antigenic peptide, at position 2 and the C terminus (3, 4), must be deeply accommodated into specific pockets of the antigen recognition site of the HLA class I molecule to stabilize the nascent complexes (5, 6) and allow for their subsequent transport to the cell membrane where they are exposed for CTL recognition (7).Human respiratory syncytial virus (HRSV) (8), a member of the Paramyxoviridae family, is the single most important cause of bronchiolitis and pneumonia in infants and young children (9–11). Infections of this virus occur in people of all ages, but although usually mild infections are reported in healthy adults, HRSV poses a serious health risk in immunocompromised individuals (12, 13) and in the elderly (14, 15). The single-stranded, negative-sense RNA genome of this enveloped virus codes for 11 proteins.Although the immune mechanism involved in HRSV disease and protection is not well understood, specific CD8⁺ T lymphocytes are required for the clearance of virus-infected cells (16). Previously, several HRSV epitopes restricted by different HLA class I molecules were identified using CTLs from seropositive individuals (17–21). However, these experiments were performed with synthetic peptides against individual proteins. In contrast, only one published study attempted to elucidate the nature and diversity of the possible array of HRSV ligands restricted by individual HLA molecules (22). In this study, virus-infected cells were cultured with stable, isotope-labeled amino acids, which were expected to act as anchor residues for the HLA allele of interest. The MHC molecules were then immunoprecipitated, and mass spectrometry analysis was performed. This study identified one HRSV ligand for each of the HLA-A2 and -B7 class I molecules (22). Therefore, is only one HRSV ligand restricted by a single HLA molecule exposed on the cell membrane surface as suggested by this study? Conversely, could a particular HLA molecule bind several ligands of this small virus simultaneously? To answer these questions, we compared HLA-B27 ligands isolated from large amounts of healthy or HRSV-infected cells without any methodological bias (selection of individual protein, use of HLA consensus scoring algorithms, etc.). This analysis demonstrated the existence of diverse, naturally processed HLA-B27 ligands from six different HRSV proteins in infected cells.     

The Effect of Proteasome Inhibition on the Generation of the Human Leukocyte Antigen (HLA) Peptidome

The Major histocompatibility complex (MHC) class I peptidome is thought to be generated mostly through proteasomal degradation of cellular proteins, a notion that is based on the alterations in presentation of selected peptides following proteasome inhibition. We evaluated the effects of proteasome inhibitors, epoxomicin and bortezomib, on human cultured cancer cells. Because the inhibitors did not reduce the level of presentation of the cell surface human leukocyte antigen (HLA) molecules, we followed their effects on the rates of synthesis of both HLA peptidome and proteome of the cells, using dynamic stable isotope labeling in tissue culture (dynamic-SILAC). The inhibitors reduced the rates of synthesis of most cellular proteins and HLA peptides, yet the synthesis rates of some of the proteins and HLA peptides was not decreased by the inhibitors and of some even increased. Therefore, we concluded that the inhibitors affected the production of the HLA peptidome in a complex manner, including modulation of the synthesis rates of the source proteins of the HLA peptides, in addition to their effect on their degradation. The collected data may suggest that the current reliance on proteasome inhibition may overestimate the centrality of the proteasome in the generation of the MHC peptidome. It is therefore suggested that the relative contribution of the proteasomal and nonproteasomal pathways to the production of the MHC peptidome should be revaluated in accordance with the inhibitors effects on the synthesis rates of the source proteins of the MHC peptides.The repertoires and levels of peptides, presented by the major histocompatibility complex (MHC)¹ class I molecules at the cells'' surface, are modulated by multiple factors. These include the rates of synthesis and degradation of their source proteins, the transport efficacy of the peptides through the transporter associated with antigen processing (TAP) into the endoplasmic reticulum (ER), their subsequent processing and loading onto the MHC molecules within the ER, and the rates of transport of the MHC molecules with their peptide cargo to the cell surface. The off-rates of the presented peptides, the residence time of the MHC complexes at the cell surface, and their retrograde transport back into the cytoplasm, influence, as well, the presented peptidomes (reviewed in (1)). Even though significant portions of the MHC class I peptidomes are thought to be derived from newly synthesized proteins, including misfolded proteins, defective ribosome products (DRiPs), and short lived proteins (SLiPs), most of the MHC peptidome is assumed to originate from long-lived proteins, which completed their functional cellular roles or became defective (retirees), (reviewed in (2)).The main protease, supplying the MHC peptidome production pipeline, is thought to be the proteasome (3). It is also responsible for generation of the final carboxyl termini of the MHC peptides (4), (reviewed in (5)). The final trimming of the n-termini of the peptides, within the endoplasmic reticulum (ER), is thought to be performed by amino peptidases, such as ERAP1/ERAAP, which fit the peptides into their binding groove on the MHC molecules (6) (reviewed in (7)). Nonproteasomal proteolytic pathways were also suggested as possible contributors to the MHC peptidome, including proteolysis by the ER resident Signal peptide peptidase (8, 9), the cytoplasmic proteases Insulin degrading enzyme (10), Tripeptidyl peptidase (11–13), and a number of proteases within the endolysosome pathway (reviewed recently in (14–17)). In contrast to the mostly cytoplasmic and ER production of the MHC class I peptidome, the class II peptidome is produced in a special compartment, associated with the endolysosome pathway (18–20). This pathway is also thought to participate in the cross presentation of class I peptides, derived from proteins up-taken by professional antigen presenting cells (21), (reviewed in (15–17, 22)).The centrality of the proteasomes in the generation of the MHC peptidome was deduced mostly from the observed change in presentation levels of small numbers of selected peptides, following proteasome inhibition (3, 23). Even the location of some of the genes encoding the catalytic subunits of the immunoproteasome (LMP2 and LMP7) (24) within the MHC class II genomic locus, was suggested to support the involvement of the proteasome in the generation of the MHC class I peptidome (25). Similar conclusions were deduced from alterations in peptide presentation, following expression of the catalytic subunits of the immunoproteasome (26), (reviewed in (5)). Yet, although most of the reports indicated reductions in presentation of selected peptides by proteasome inhibition (3, 27–29), others have observed only limited, and sometimes even opposite effects (23, 30–32).The matter is further complicated by the indirect effects of proteasome inhibition used for such studies on the arrest of protein synthesis by the cells (33–35), on the transport rates of the MHC molecules to the cell surface, and on their retrograde transport back to the vesicular system (36) (reviewed in (37)). Proteasome inhibition likely causes shortage of free ubiquitin, reduced supply of free amino acids, and induces an ER unfolded protein response (UPR), which signals the cells to block most (but not all) cellular protein synthesis (reviewed in (38)). Because a significant portion of the MHC peptidome originates from degradation of DRiPs and SLiPs (reviewed in (2)), arrest of new protein synthesis should influence the presentation of their derived MHC peptides. Taken together, these arguments may suggest that merely following the changes in the presentation levels of the MHC molecules, or even of specific MHC peptides, after proteasome inhibition, does not provide the full picture for deducing the relative contribution of the proteasomal pathway to the production of the MHC peptidome (reviewed in (7)).MHC peptidome analysis can be performed relatively easily by modern capillary chromatography combined with mass spectrometry (reviewed in (39)). The peptides are recovered from immunoaffinity purified MHC molecules after detergent solubilization of the cells (40, 41), from soluble MHC molecules secreted to the cells'' growth medium (42, 43) or from patients'' plasma (44). The purified peptides pools are resolved by capillary chromatography and the individual peptides are identified and quantified by tandem mass spectrometry (40), (reviewed in (45–47)). In cultured cells, quantitative analysis can also be followed by metabolic incorporation of stable isotope labeled amino acids (SILAC) (48). Furthermore, the rates of de novo synthesis of both MHC peptides and their proteins of origin can be followed using the dynamic-SILAC proteomics approach (49) with its further adaptation to HLA peptidomics (50–52).This study attempts to define the relative contribution of the proteasomes to the production of HLA class I peptidome by simultaneously following the effects of proteasome inhibitors, epoxomicin and bortezomib (Velcade), on the rates of de novo synthesis of both the HLA class I peptidome and the cellular proteome of the same MCF-7 human breast cancer cultured cells. The proteasome inhibitors did not reduce the levels of HLA presentations, yet affected the rates of production of both the HLA peptidome and cellular proteome, mostly decreasing, but also increasing some of the synthesis rates of the HLA peptides and cellular proteins. Thus, we suggest that the degree of contribution of the proteasomal pathway to the production of the HLA-I peptidome should be re-evaluated in accordance with their effects on the entire HLA class-I peptidome, while taking into consideration the inhibitors'' effects on the synthesis (and degradation) rates of the source proteins of each of the studied HLA peptides.     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]