Early modification of host cell gene expression induced by HIV-1

Glioma pathogenesis-related protein 1 performs dual functions in tumor cells

Glioma pathogenesis-related protein 1 (GLIPR1) was identified as an oncoprotein in some cancer types including gliomas, breast cancers, melanoma cancers, and Wilms tumors, but as a tumor suppressor in some other types of cancers, such as prostate cancers, lung cancers, bladder cancers, and thyroid cancers. In gliomas, GLIPR1 promotes the migration and invasion of glioma cells by interaction with the actin polymerization regulator Neural Wiskott-Aldrich syndrome protein (N-WASP) and then abolishes the negative effects of Heterogeneous nuclear ribonuclear protein K (hnRNPK). In prostate cancers, high levels of GLIPR1 induce apoptosis and destruction of oncoproteins. In lung cancers, overexpression of GLIPR1 inhibits the growth of lung cancer cells partially through inhibiting the V-ErbB avian erythroblastic leukemia viral oncogene homolog3 (ErbB3) pathway. However, the mechanisms that GLIPR1 performs its function in other tumors still remain unclear. The tumor suppressing role of GLIPR1 has been explored to the cancer treatment. The adenoviral vector-mediated Glipr1 (AdGlipr1) gene therapy and the GLIPR1-transmembrane domain deleted (GLIPR1-ΔTM) protein therapy both showed antitumor activities and stimulated immune response in prostate cancers. Whether GLPIR1 can be used to treat other tumors is an important topic to be explored. Among which, whether GLPIR1 can be used to treat lung cancer by atomizing inhalation is the key topic we care about. If it does, this therapy has a wide application prospect and is a great progression in lung cancer treatment.

The Role of a Nascent Polypeptide-Associated Complex Subunit Alpha in Siderophore Biosynthesis, Oxidative Stress Response, and Virulence in Alternaria alternata

The present study demonstrates that a nascent polypeptide-associated complex α subunit (Nac1) functions as a transcriptional regulator and plays both positive and negative roles in a vast array of functions in Alternaria alternata. Gain- and loss-of-function studies reveal that Nac1 is required for the formation and germination of conidia, likely via the regulation of Fus3 and Slt2 mitogen-activated protein kinase (MAPK)-coding genes, both implicated in conidiation. Nac1 negatively regulates hyphal branching and the production of cell wall-degrading enzymes. Importantly, Nac1 is required for the biosynthesis of siderophores, a novel phenotype that has not been reported to be associated with a Nac in fungi. The expression of Nac1 is positively regulated by iron, as well as by the Hog1 MAPK and the NADPH-dependent oxidase (Nox) complex. Nac1 confers cellular susceptibility to reactive oxygen species (ROS) likely via negatively regulating the expression of the genes encoding Yap1, Skn7, Hog1, and Nox, all involved in ROS resistance. The involvement of Nac1 in sensitivity to glucose-, mannitol-, or sorbitol-induced osmotic stress could be due to its ability to suppress the expression of Skn7. The requirement of Nac1 in resistance to salts is unlikely mediated through the transcriptional activation of Hog1. Although Nac1 plays no role in toxin production, Nac1 is required for fungal full virulence. All observed deficiencies can be restored by re-expressing a functional copy of Nac1, confirming that Nac1 contributes to the phenotypes. Thus, a dynamic regulation of gene expression via Nac1 is critical for developmental, physiological, and pathological processes of A. alternata.

All-Round Manipulation of the Actin Cytoskeleton by HIV

While significant progress has been made in terms of human immunodeficiency virus (HIV) therapy, treatment does not represent a cure and remains inaccessible to many people living with HIV. Continued mechanistic research into the viral life cycle and its intersection with many aspects of cellular biology are not only fundamental in the continued fight against HIV, but also provide many key observations of the workings of our immune system. Decades of HIV research have testified to the integral role of the actin cytoskeleton in both establishing and spreading the infection. Here, we review how the virus uses different strategies to manipulate cellular actin networks and increase the efficiency of various stages of its life cycle. While some HIV proteins seem able to bind to actin filaments directly, subversion of the cytoskeleton occurs indirectly by exploiting the power of actin regulatory proteins, which are corrupted at multiple levels. Furthermore, this manipulation is not restricted to a discrete class of proteins, but rather extends throughout all layers of the cytoskeleton. We discuss prominent examples of actin regulators that are exploited, neutralized or hijacked by the virus, and address how their coordinated deregulation can lead to changes in cellular behavior that promote viral spreading.

Identification and expression analysis of nascent polypeptide-associated complex alpha gene in response to immune challenges in Japanese flounder Paralichthys olivaceus

Nascent polypeptide-associated complex (NAC) is a conserved heterodimeric protein consisting of alpha and beta subunits. In addition to acting as a protein translation chaperone by forming a heterodimer with the beta subunit, NAC alpha (NACA) also shows important immune significance independent of NAC beta in mammalian cells. In lower vertebrates, however, the immunological relevance of NACA has not been revealed yet. In the present study, we identified and characterized a NACA gene (termed poNACA) involved in innate immune response in Japanese flounder Paralichthys olivaceus. poNACA encodes a 215-amino-acid protein, with an apparent molecular weight of 23.5 kDa and an isoelectric point of 4.51. Tissue distribution analysis revealed that poNACA gene was constitutively expressed in all examined tissues and showed dominant expression in hepatopancreas and gonad tissues. In enriched Japanese flounder head kidney macrophages and peripheral blood leucocytes, the expression of poNACA mRNA transcript was significantly induced by LPS, Poly(I:C) and zymosan stimulations. In vivo experiments further revealed that poNACA gene expression was up-regulated in head kidney, gill and spleen tissues in response to Edwardsiella tarda challenges. Furthermore, overexpression of poNACA in Japanese flounder FG-9307 cells resulted in increased gene expression of IL-1beta, IL-11 and TNF-alpha, and myxovirus resistance (Mx). Taken together, our findings indicate that an immune response gene, poNACA, involved in innate immune regulation in P. olivaceus has been identified.

Exploring the roles of basal transcription factor 3 in eukaryotic growth and development

Basal transcription factor 3 (BTF3) has been reported to play a significant part in the transcriptional regulation linking with eukaryotes growth and development. Alteration in the BTF3 gene expression patterns or variation in their activities adds to the explanation of different signaling pathways and regulatory networks. Moreover, BTF3s often respond to numerous stresses, and subsequently they are involved in regulation of various mechanisms. BTF3 proteins also function through protein-protein contact, which can assist us to identify the multifaceted processes of signaling and transcriptional regulation controlled by BTF3 proteins. In this review, we discuss current advances made in starting to explore the roles of BTF3 transcription factors in eukaryotes especially in plant growth and development.

Knockdown of ERM family member moesin in host cells increases HIV type 1 replication

Moesin is a member of the ERM (ezrin, radixin, moesin) family of cytoskeleton/membrane structure organizing and signal transduction proteins. Previously, we found an increased expression of moesin during HIV-1 infection. Moesin was also reported to be incorporated into HIV-1 virions. To analyze whether moesin is a host factor affecting the replication cycle of human immunodeficiency virus type 1 (HIV-1), we used small interfering RNAs (siRNAs) to evaluate the effect of moesin knockdown on HIV-1 replication in P4-CCR5 cells. Moesin's knockdown did not affect the cell viability or cell phenotype. Interestingly, we observed a marked increase in viral replication, as demonstrated by enhanced HIV-1 RNA, p24 antigen, and ß-galactosidase reporter expression. Moesin-dependent enhancement of HIV-1 replication was confirmed in lymphocytic host cells (Jurkat). These results suggest an overall rather restrictive role of moesin for HIV-1 replication in host cells in vitro.

HIV-1 infection suppresses expression of host cell cycle-associated gene PDS5A

OBJECTIVE

To unravel the interplay between HIV-1 and its host cell, the effect of HIV-1 infection on cellular gene expression was investigated.

METHODS

HIV-1(SF33)-infected and uninfected H9 T cells were screened by differential display and RNase protection assay. The finding (PDS5A) was confirmed in HIV-1(Lai)-infected P4-CCR5 HeLa cells, which were also examined after PDS5A siRNA knockdown in regard to HIV-1 replication by quantitative RT-PCR, p24 ELISA and LTR-driven β-galactosidase expression. The PDS5A knockdown effect on cellular gene expressions was studied by microarray analysis. PDS5A tissue expression was determined by Northern blotting.

RESULTS

Regulator of cohesion maintenance, homolog A (PDS5A) was found to be down-regulated by HIV-1. When PDS5A was suppressed by siRNA, HIV-1 replication was unaffected. PDS5A was found to be highly expressed in skeletal muscle tissue, and to lesser degrees in pancreas, heart, placenta, lung, kidney, liver and brain. Microarray analysis of PDS5A knockdown revealed 91 differential gene products over-representing cell cycle, transport and protein stability regulation, including 4 genes (PP2A, RANTES, PCAF, TCF7L2) previously reported to interact with HIV-1.

CONCLUSION

The data show a downregulation of proliferation-associated host gene PDS5A and suggest a role of PDS5A in HIV-1-induced cellular pathogenesis but not viral replication.

Inhibition of X4-tropic HIV type 1 replication by knockdown of the cellular protein LEREPO4

Human immunodeficiency virus 1 (HIV-1) and host cell factors show important mutual interactions. We found that HIV-1 infection induced expression of a likely ortholog of mouse immediate early response erythropoietin 4 (LEREPO4) in vitro. When LEREPO4 expression was suppressed by siRNA in P4-CCR5 cells, HIV-1 replication showed significantly reduced HIV-1 transcript and p24 protein levels as measured by quantitative PCR and ELISA, respectively. The LEREPO4 knockdown also had an inhibitory effect on HIV-1-LTR-driven reporter plasmid expression of β-galactosidase. Furthermore, the inhibitory effect of LEREPO4 silencing on HIV-1 replication was confirmed in Jurkat T cells. The up-regulation of LEREPO4 by HIV-1 and the inhibition of HIV-1 replication mediated by knockdown of LEREPO4 may point to an important functional role of LEREPO4 as a novel HIV-1 dependency factor.

Crystal structures of NAC domains of human nascent polypeptide-associated complex (NAC) and its αNAC subunit

Nascent polypeptide associated complex (NAC) and its two isolated subunits, αNAC and βNAC, play important roles in nascent peptide targeting. We determined a 1.9 Å resolution crystal structure of the interaction core of NAC heterodimer and a 2.4 Å resolution crystal structure of αNAC NAC domain homodimer. These structures provide detailed information of NAC heterodimerization and αNAC homodimerization. We found that the NAC domains of αNAC and βNAC share very similar folding despite of their relative low identity of amino acid sequences. Furthermore, different electric charge distributions of the two subunits at the NAC interface provide an explanation to the observation that the heterodimer of NAC complex is more stable than the single subunit homodimer. In addition, we successfully built a βNAC NAC domain homodimer model based on homologous modeling, suggesting that NAC domain dimerization is a general property of the NAC family. These 3D structures allow further studies on structure-function relationship of NAC.

Dual binding mode of the nascent polypeptide-associated complex reveals a novel universal adapter site on the ribosome

Nascent polypeptide-associated complex (NAC) was identified in eukaryotes as the first cytosolic factor that contacts the nascent polypeptide chain emerging from the ribosome. NAC is present as a homodimer in archaea and as a highly conserved heterodimer in eukaryotes. Mutations in NAC cause severe embryonically lethal phenotypes in mice, Drosophila melanogaster, and Caenorhabditis elegans. In the yeast Saccharomyces cerevisiae NAC is quantitatively associated with ribosomes. Here we show that NAC contacts several ribosomal proteins. The N terminus of betaNAC, however, specifically contacts near the tunnel exit ribosomal protein Rpl31, which is unique to eukaryotes and archaea. Moreover, the first 23 amino acids of betaNAC are sufficient to direct an otherwise non-associated protein to the ribosome. In contrast, alphaNAC (Egd2p) contacts Rpl17, the direct neighbor of Rpl31 at the ribosomal tunnel exit site. Rpl31 was also recently identified as a contact site for the SRP receptor and the ribosome-associated complex. Furthermore, in Escherichia coli peptide deformylase (PDF) interacts with the corresponding surface area on the eubacterial ribosome. In addition to the previously identified universal adapter site represented by Rpl25/Rpl35, we therefore refer to Rpl31/Rpl17 as a novel universal docking site for ribosome-associated factors on the eukaryotic ribosome.

Inhibition of HIV-1 replication by small interfering RNAs directed against glioma pathogenesis related protein (GliPR) expression

BACKGROUND

Previously, we showed that glioma pathogenesis related protein (GliPR) is induced in CEM T cells upon HIV-1 infection in vitro. To examine whether GliPR plays a role as HIV dependency factor (HDF), we tested the effect of GliPR suppression by siRNA on HIV-1 replication.

RESULTS

Induction of GliPR expression by HIV-1 was confirmed in P4-CCR5 cells. When GliPR was suppressed by siRNA, HIV-1 replication was significantly reduced as measured by HIV-1 transcript levels, HIV-1 p24 protein levels, and HIV-1 LTR-driven reporter gene expression, suggesting that GliPR is a cellular co-factor of HIV-1. Microarray analysis of uninfected HeLa cells following knockdown of GliPR revealed, among a multitude of gene expression alterations, a down-regulation of syndecan-1, syndecan-2, protein kinase C alpha (PRKCA), the catalytic subunit beta of cAMP-dependent protein kinase (PRKACB), nuclear receptor co-activator 3 (NCOA3), and cell surface protein CD59 (protectin), all genes having relevance for HIV-1 pathology.

CONCLUSIONS

The up-regulation of GliPR by HIV-1 and the early significant inhibition of HIV-1 replication mediated by knockdown of GliPR reveal GliPR as an important HIV-1 dependency factor (HDF), which may be exploited for HIV-1 inhibition.

Mitochondrial cell death control in familial Parkinson disease

Many sporadic cases of Parkinsons disease have mutations in the PINK protein kinase, whose substrate is now revealed to be a protein that protects mitochondria from oxidative stress.

Inhibition of Alpha Nascent Polypeptide Associated Complex Protein May Induce Proliferation, Differentiation and Enhance the Cytotoxic Activity of Human CD8+ T Cells

The molecular mechanisms that control CD8(+) T cell proliferation and differentiations are poorly understood. Consequently, better understanding of the molecular pathways that regulate these processes may have an impact on the numbers and efficiency of antigen-specific cells that can be generated for cellular immunotherapy applications. Using differential display, we previously determined that alpha nascent polypeptide associated complex (alpha NAC) was identified as a potential target as its protein expression was found to be down-regulated as differentiation progressed in cultured human CD8(+) T cells. Here anti-sense technology was used to further investigate the role which alpha NAC may play in proliferation and differentiation. Human purified CD8(+) T cells were cultured in the presence of sense, non-sense and anti-sense oligonucleotides against the mRNA of alpha NAC. We reported that in the presence of anti-sense oligonucleotides expanded CD8(+) T cells exhibited higher levels of differentiation and activation markers and also increased proliferation response compared to cells cultured with sense-oligonucleotides. Furthermore, the functional cytotoxicity of CD8(+) T cells cultured with anti-sense was increased to 66% (+/-4.7%) compared to 42% (+/-3.2%) in cells expanded in the presence of oligonucleotides controls. Taken together, our results demonstrated that inhibition of alpha NAC protein induced not only cell proliferation but also differentiation and cytotoxic activity of CD8(+) T cells.

Mitochondrial complex I activity is impaired during HIV-1-induced T-cell apoptosis

Studies carried out till date to elucidate the pathways involved in HIV-1-induced T-cell depletion has revealed that apoptosis underlie the etiology, however, a clear molecular understanding of HIV-1-induced apoptosis has remained elusive. Although evidences pointing towards the importance of mitochondrial energy generating system in apoptosis exist but it's exact role remains to be clearly understood. Here, we describe for the first time specific downregulation of a complex I subunit NDUFA6 with simultaneous impairment of mitochondrial complex I activity in HIV infection. We also show that NDUFA6 gene silencing induces apoptosis and its overexpression reduces apoptosis in HIV-infected cells. Finally, sensitivity to complex I inhibitor Rotenone is reduced in HIV-1-infected T cells indicating an important role for it in the death process. Our data provide a novel molecular basis as to how the virus might interfere with host cell energy generating system during apoptotic cell death.

Gene expression changes induced by a recombinant E1-/E3- adenovirus type 5 vector in human mammary epithelial cells

OBJECTIVES

Adenoviral vectors are used in transferring exogenous genes to a variety of cells and tissue types both in vitro and in vivo. Gene expression changes induced by an E1/E3-defective adenovirus vector have been studied in human mammary epithelial cells by comparing the gene expression profile in infected and uninfected cells.

METHODS

The human mammary epithelial cell line HB2 was infected with an E1/E3-defective adenovirus type 5 vector. Total RNA was extracted from infected and uninfected cells 24 and 72 h after infection and subjected to microarray analysis using the Affymetrix U133A genomic chip system. Semiquantitative RT-PCR confirmed the regulation of genes observed by microarray analysis.

RESULTS

The microarray analysis showed 24 and 95 transcripts to be regulated 24 and 72 h after infection, respectively. A relatively high number of genes involved in innate and inflammatory host immune responses, including interleukin-8, interleukin-6, NF-kappaB(2), RELB and fos, were induced. As expected from an E1-defective virus, changes in the expression of genes involved in the G1-S transition and in the activation of cell proliferation were not detected.

CONCLUSION

Our study provides insight into the host transcriptional response following transduction of an adenoviral vector into mammary epithelial cells.

The Crystal Structure of Archaeal Nascent Polypeptide-associated Complex (NAC) Reveals a Unique Fold and the Presence of a Ubiquitin-associated Domain

Nascent polypeptide-associated complex (NAC) was identified in eukaryotes as the first cytosolic factor that contacts the nascent polypeptide chain emerging from the ribosome. NAC is highly conserved from yeast to humans. Mutations in NAC cause severe embryonically lethal phenotypes in mice, Drosophila, and Caenorhabditis elegans. NAC was suggested to protect the nascent chain from inappropriate early interactions with cytosolic factors. Eukaryotic NAC is a heterodimer with two subunits sharing substantial homology with each other. All sequenced archaebacterial genomes exhibit only one gene homologous to the NAC subunits. Here we present the first archaebacterial NAC homolog. It forms a homodimer, and as eukaryotic NAC it is associated with ribosomes and contacts the emerging nascent chain on the ribosome. We present the first crystal structure of a NAC protein revealing two structural features: (i) a novel unique protein fold that mediates dimerization of the complex, and (ii) a ubiquitin-associated domain that suggests a yet unidentified role for NAC in the cellular protein quality control system via the ubiquitination pathway. Based on the presented structure we propose a model for the eukaryotic heterodimeric NAC domain.

Impact on genetic networks in human macrophages by a CCR5 strain of human immunodeficiency virus type 1

Human immunodeficiency virus type 1 (HIV-1) impacts multiple lineages of hematopoietic cells, including lymphocytes and macrophages, either by direct infection or indirectly by perturbations of cell networks, leading to generalized immune deficiency. We designed a study to discover, in primary human macrophages, sentinel genetic targets that are impacted during replication over the course of 7 days by a CCR5-using virus. Expression of mRNA and proteins in virus- or mock-treated macrophages from multiple donors was evaluated. Hierarchical agglomerative cluster analysis grouped into distinct temporal expression patterns >900 known human genes that were induced or repressed at least fourfold by virus. Expression of more than one-third of the genes was induced rapidly by day 2 of infection, while other genes were induced at intermediate (day 4) or late (day 7) time points. More than 200 genes were expressed exclusively in either virus- or mock-treated macrophage cultures, independent of the donor, providing an unequivocal basis to distinguish an effect by virus. HIV-1 altered levels of mRNA and/or protein for diverse cellular programs in macrophages, including multiple genes that can contribute to a transition in the cell cycle from G(1) to G(2)/M, in contrast to expression in mock-treated macrophages of genes that maintain G(0)/G(1). Virus treatment activated mediators of cell cycling, including PP2A, which is impacted by Vpr, as well as GADD45 and BRCA1, potentially novel targets for HIV-1. The results identify interrelated programs conducive to optimal HIV-1 replication and expression of genes that can contribute to macrophage dysfunction.

Heat-shock protein 70 exerts opposing effects on Vpr-dependent and Vpr-independent HIV-1 replication in macrophages

HIV-1 viral protein R (Vpr) shuttles between the nucleus and the cytoplasm and is believed to contribute to the process of nuclear translocation of the viral preintegration complex, thus facilitating HIV-1 replication in macrophages. In this report, we demonstrate that Hsp70, a heat-shock protein contributing to cellular stress responses, inhibits nuclear translocation of HIV-1 Vpr. In macrophages, Hsp70 is induced shortly after HIV-1 infection. Recombinant Hsp70 or a mild heat shock diminished replication of the wild-type HIV-1, suggesting that Hsp70 might function as an innate antiviral factor. Surprisingly, Hsp70 stimulated nuclear import and replication in macrophages of the Vpr-deficient HIV-1 construct. This finding suggests that Hsp70 and Vpr may function in a similar manner when expressed separately, but they neutralize each other's activity when present together. Consistent with this interpretation, Hsp70 coprecipitated with Vpr from HIV-1–infected cells.

Identification of novel expressed sequences, up-regulated in the leucocytes of chronic fatigue syndrome patients

BACKGROUND

Chronic fatigue syndrome (CFS) is an increasing medical phenomenon of unknown aetiology leading to high levels of chronic morbidity. Of the many hypotheses that purport to explain this disease, immune system activation, as a central feature, has remained prominent but unsubstantiated. Supporting this, a number of important cytokines have previously been shown to be over-expressed in disease subjects. The diagnosis of CFS is highly problematic since no biological markers specific to this disease have been identified. The discovery of genes relating to this condition is an important goal in seeking to correctly categorize and understand this complex syndrome.

OBJECTIVE

The aim of this study was to screen for changes in gene expression in the lymphocytes of CFS patients.

METHODS

'Differential Display' is a method for comparing mRNA populations for the induction or suppression of genes. In this technique, mRNA populations from control and test subjects can be 'displayed' by gel electrophoresis and screened for differing banding patterns. These differences are indicative of altered gene expression between samples, and the genes that correspond to these bands can be cloned and identified. Differential display has been used to compare expression levels between four control subjects and seven CFS patients.

RESULTS

Twelve short expressed sequence tags have been identified that were over-expressed in lymphocytes from CFS patients. Two of these correspond to cathepsin C and MAIL1 - genes known to be upregulated in activated lymphocytes. The expression level of seven of the differentially displayed sequences have been verified by quantifying relative level of these transcripts using TAQman quantitative PCR.

CONCLUSION

Taken as a whole, the identification of novel gene tags up-regulated in CFS patients adds weight to the idea that CFS is a disease characterized by subtle changes in the immune system.

Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines

The expression levels of approximately 4,600 cellular RNA transcripts were assessed in CD4(+)-T-cell lines at different times after infection with human immunodeficiency virus type 1 strain BRU (HIV-1(BRU)) using DNA microarrays. We found that several classes of genes were inhibited by HIV-1(BRU) infection, consistent with the G(2) arrest of HIV-1-infected cells induced by Vpr. These included genes involved in cell division and transcription, a family of DEAD-box proteins (RNA helicases), and all genes involved in translation and splicing. However, the overall level of cell activation and signaling was increased in infected cells, consistent with strong virus production. These included a subgroup of transcription factors, including EGR1 and JUN, suggesting they play a specific role in the HIV-1 life cycle. Some regulatory changes were cell line specific; however, the majority, including enzymes involved in cholesterol biosynthesis, of changes were regulated in most infected cell lines. Compendium analysis comparing gene expression profiles of our HIV-1 infection experiments to those of cells exposed to heat shock, interferon, or influenza A virus indicated that HIV-1 infection largely induced specific changes rather than simply activating stress response or cytokine response pathways. Thus, microarray analysis confirmed several known HIV-1 host cell interactions and permitted identification of specific cellular pathways not previously implicated in HIV-1 infection. Continuing analyses are expected to suggest strategies for impacting HIV-1 replication in vivo by targeting these pathways.

Novel strategy for anti-HIV-1 action: selective cytotoxic effect of N-myristoyltransferase inhibitor on HIV-1-infected cells

N-myristoyltransferase (NMT) is essential for the survival of eukaryotes and the production of infectious human immunodeficiency virus type-1(HIV-1) by the host cell. In this study, we found decreases in the mRNA levels of human NMT isoforms and the NMT activities in the course of HIV-1 infection in the human T-cell line, CEM. Investigating the cytotoxic effect of the novel synthetic NMT inhibitors on the chronic HIV-1 infected T-cell line, CEM/LAV-1, and the uninfected CEM, revealed that the cytotoxic effect was significantly selective for CEM/LAV-1. This was thought to be due to the difference between the NMT levels of the cell lines. In this paper, we propose that NMT may be a candidate target for anti-HIV-1-infected-cell agents.

Down-regulation of N-myristoyl transferase expression in human T-cell line CEM by human immunodeficiency virus type-1 infection

The present study focuses on the expression level of N-myristoyl transferase (NMT) in the course of human immunodeficiency virus type-1 (HIV-1) infection. HIV-1 structural proteins were gradually expressed during the process of infection of the human T-cell line CEM, whereas the expression levels of NMT subsequently decreased under the same conditions. In addition, the chronically HIV-1-infected T-cell line CEM/LAV-1 exhibited low expression levels of NMT. We hypothesize that the decrease in the expression level of NMT due to HIV-1 infection may be related to the virus' strategy that leads to its persistent replication.

Use of serial analysis of gene expression (SAGE) technology

Serial analysis of gene expression, or SAGE, is an experimental technique designed to gain a direct and quantitative measure of gene expression. The SAGE method is based on the isolation of unique sequence tags (9-10 bp in length) from individual mRNAs and concatenation of tags serially into long DNA molecules for a lump-sum sequencing. The SAGE method can be applied to the studies exploring virtually any kinds of biological phenomena in which the changes in cellular transcription are responsible. SAGE is a highly competent technology that can not only give a global gene expression profile of a particular type of cell or tissue, but also help us identify a set of specific genes to the cellular conditions by comparing the profiles constructed for a pair of cells that are kept at different conditions. In this review, we present an outline of the original method, several studies achieved by using the method as a major strategic tool, technological difficulties and intrinsic problems that emerged, and improvements and modifications of the method to cope with these drawbacks. We then present our modified SAGE procedure that generates longer sequence tags (14 bp) rather in detail, and the profile (80K profile) derived from HeLa cells that is composed of 80000 tags obtained from a single library. In addition, a series of smaller profiles (2, 4, 10, 20 and 40K) was made by dividing the 80K profile. When we compared these smaller profiles with respect to tag counts for a number of genes, it became apparent that counts of most gene tags increase stably and constantly as the size of profiles increase, while several genes do not. This may be another problem we have to keep in mind, when the profiles are compared for the identification of 'specific genes'.

Mitochondrial control of cell death induced by HIV-1-encoded proteins

In most examples of physiological or pathological cell death, mitochondrial membrane permeabilization (MMP) constitutes an early critical event of the lethal process. Signs of MMP that precede nuclear apoptosis include the translocation of cytochrome c and apoptosis-inducing factor (AIF) from mitochondria to an extra-mitochondrial localization, as well as the dissipation of the mitochondrial transmembrane potential. MMP also occurs in HIV-1-induced apoptosis. Different HIV-1 encoded proteins (Env, Vpr, Tat, PR) can directly or indirectly trigger MMP, thereby causing cell death. The gp120/gp41 Env complex constitutes an example for an indirect MMP inducer. Env expressed on the plasma membrane of HIV-1 infected (or Env-transfected) cells mediates cell fusion with CD4/CXCR4-expressing uninfected cells. After a cell type-dependent latency period, syncytia then undergo MMP and apoptosis. Vpr exemplifies a direct MMP inducer. Vpr binds to the adenine nucleotide translocator (ANT), a mitochondrial inner membrane protein which also interacts with apoptosis-regulatory proteins from the Bcl-2/Bax family. Binding of Vpr to ANT favors formation of a non-specific pore leading to MMP. The structural motifs of the Vpr protein involved in MMP are conserved among most pathogenic HIV-1 isolates and determine the cytotoxic effect of Vpr. These data suggest the possibility that viruses employ multiple strategies to regulate host cell apoptosis by targeting mitochondria.

Identification and characterization of differentially expressed mRNAs in HIV type 1-infected human T cells

We used a novel differential display (DD) technique to identify host factors involved in virus replication, pathogenesis, and host response in HIV-1-infected T cells. Thirteen cDNA fragments differentially expressed in HIV-1NL4-3-infected MT-4 cells prior to the occurrence of specific apoptotic cell death were sequenced and identified. Two of seven elevated genes were identical to HIV-1 sequences and the other five were MIP-1alpha, ACTE-III, CD11c, arginase I, and CCR5. The six downregulated genes included prothymosin-a, Jaw-1, proteasome subunit XAPC7, splicing factor 9G8, GA17 protein, and an unknown mRNA. Northern blot and RT-PCR analyses confirmed the altered gene expressions in MT-4 cells as well as in another T cell line, MOLT-4. We also revealed that the amount of MIP-1alpha in culture supernatant of HIV-1-infected cells was increased by more than 15-fold relative to control cells, and the expression of its receptor CCR5 was cooperatively upregulated on the surface of these cells. Furthermore, the upregulation of CD11c after HIV-1 infection was slightly inhibited by blocking the MIP-1alpha-mediated signal transduction. These results indicate that genes altered on HIV-1 infection may be mutually organized and play an important role in HIV-1-induced pathogenesis.

Serial analysis of gene expression in HIV-1-infected T cell lines

The gene expression profile of the HIV-1 infection state was analyzed in the human T cell line MOLT-4. Using the serial analysis of gene expression (SAGE) method, a total of 142¿ omitted¿603 SAGE tags were sequenced and identified, representing 43¿ omitted¿581 unique mRNA species. Comparison of expression patterns revealed that 53 cellular genes were differentially expressed upon HIV-1 infection. Northern blot and RT-PCR analyses confirmed the altered expression of the genes in both MOLT-4 and MT-4 cells. Up-regulated genes were mainly composed of transcription factors and genes related to T cell activation, whereas down-regulated genes were comprised of mitochondrial proteins, actin-related factors and translational factors. These findings indicate that persistent T cell activation, which may accelerate HIV-1 replication, and the disruption of cellular housekeeping genes including those involved in anti-apoptotic systems, may play an important role in HIV-1-induced pathogenesis.