The alpha chain of the nascent polypeptide-associated complex functions as a transcriptional coactivator

Identifying Methylation Signatures and Rules for COVID-19 With Machine Learning Methods

The occurrence of coronavirus disease 2019 (COVID-19) has become a serious challenge to global public health. Definitive and effective treatments for COVID-19 are still lacking, and targeted antiviral drugs are not available. In addition, viruses can regulate host innate immunity and antiviral processes through the epigenome to promote viral self-replication and disease progression. In this study, we first analyzed the methylation dataset of COVID-19 using the Monte Carlo feature selection method to obtain a feature list. This feature list was subjected to the incremental feature selection method combined with a decision tree algorithm to extract key biomarkers, build effective classification models and classification rules that can remarkably distinguish patients with or without COVID-19. EPSTI1, NACAP1, SHROOM3, C19ORF35, and MX1 as the essential features play important roles in the infection and immune response to novel coronavirus. The six significant rules extracted from the optimal classifier quantitatively explained the expression pattern of COVID-19. Therefore, these findings validated that our method can distinguish COVID-19 at the methylation level and provide guidance for the diagnosis and treatment of COVID-19.

Fidelity of Cotranslational Protein Targeting to the Endoplasmic Reticulum

Fidelity of protein targeting is essential for the proper biogenesis and functioning of organelles. Unlike replication, transcription and translation processes, in which multiple mechanisms to recognize and reject noncognate substrates are established in energetic and molecular detail, the mechanisms by which cells achieve a high fidelity in protein localization remain incompletely understood. Signal recognition particle (SRP), a conserved pathway to mediate the localization of membrane and secretory proteins to the appropriate cellular membrane, provides a paradigm to understand the molecular basis of protein localization in the cell. In this chapter, we review recent progress in deciphering the molecular mechanisms and substrate selection of the mammalian SRP pathway, with an emphasis on the key role of the cotranslational chaperone NAC in preventing protein mistargeting to the ER and in ensuring the organelle specificity of protein localization.

Lnc-GD2H Promotes Proliferation by Forming a Feedback Loop With c-Myc and Enhances Differentiation Through Interacting With NACA to Upregulate Myog in C2C12 Myoblasts

In the present study, the roles of a novel long non-coding RNA (lncRNA), lnc-GD2H, in promoting C2C12 myoblast proliferation and differentiation and muscle regeneration were investigated by quantitative polymerase chain reaction, western blotting, Cell Counting Kit-8, 5-ethynyl-2′-deoxyuridine (EdU), immunofluorescence staining, luciferase reporter, mass spectrometry, pulldown, chromatin immunoprecipitation, RNA immunoprecipitation assay, wound healing assays, and cardiotoxin (CTX)-induced muscle injury assays. It was observed that lnc-GD2H promoted myoblast proliferation as evidenced by the enhancement of the proliferation markers c-Myc, CDK2, CDK4, and CDK6, percentage of EdU-positive cells, and rate of cell survival during C2C12 myoblast proliferation. Additional experiments confirmed that c-Myc bound to the lnc-GD2H promoter and regulated its transcription. lnc-GD2H promoted cell differentiation with enhanced MyHC immunostaining as well as increased expression of the myogenic marker genes myogenin (Myog), Mef2a, and Mef2c during myoblast differentiation. Additional assays indicated that lnc-GD2H interacted with NACA which plays a role of transcriptional regulation in myoblast differentiation, and the enrichment of NACA at the Myog promoter was impaired by lnc-GD2H. Furthermore, inhibition of lnc-GD2H impaired muscle regeneration after CTX-induced injury in mice. lnc-GD2H facilitated the expression of proliferating marker genes and formed a feedback loop with c-Myc during myoblast proliferation. In differentiating myoblasts, lnc-GD2H interacted with NACA to relieve the inhibitory effect of NACA on Myog, facilitating Myog expression to promote differentiation. The results provide evidence for the role of lncRNAs in muscle regeneration and are useful for developing novel therapeutic targets for muscle disorders.

Nfil3, a target of the NACA transcriptional coregulator, affects osteoblast and osteocyte gene expression differentially

Intermittent administration of PTH(1-34) has a profound osteoanabolic effect on the skeleton. At the cellular level, osteoblasts and osteocytes are two crucial cell types that respond to PTH stimulation in bone. The transcriptional cofactor Nascent polypeptide Associated Complex and coregulator alpha (NACA) is a downstream target of the PTH-Gαs-PKA axis in osteoblasts. NACA functions as a transcriptional cofactor affecting bZIP factor-mediated transcription of target promoters in osteoblasts, such as Osteocalcin (Bglap2). Here, we used RNA-Seq and ChIP-Seq against NACA in PTH-treated MC3T3-E1 osteoblastic cells to identify novel targets of the PTH-activated NACA. Our approach identified Nuclear factor interleukin-3-regulated (Nfil3) as a target promoter of this pathway. Knockdown of Naca reduced the response of Nfil3 to PTH(1-34) stimulation. In silico analysis of the Nfil3 promoter revealed potential binding sites for NACA (located within the ChIP fragment) and CREB. We show that following PTH stimulation, phosphorylated-CREB binds the proximal promoter of Nfil3 in osteoblasts. The activity of the Nfil3 promoter (-818/+182 bp) is regulated by CREB and this activation relies on the presence of NACA. In addition, we show that knockdown of Nfil3 enhances the expression of osteoblastic differentiation markers in MC3T3-E1 cells while it represses osteocytic marker gene expression in IDG-SW3 cells. These results show that the PTH-induced NACA axis regulates Nfil3 expression and suggest that NFIL3 acts as a transcriptional repressor in osteoblasts while it exhibits differential activity as an activator in osteocytes.

The beta Subunit of Nascent Polypeptide Associated Complex Plays A Role in Flowers and Siliques Development of Arabidopsis thaliana

The nascent polypeptide-associated (NAC) complex was described in yeast as a heterodimer composed of two subunits, α and β, and was shown to bind to the nascent polypeptides newly emerging from the ribosomes. NAC function was widely described in yeast and several information are also available about its role in plants. The knock down of individual NAC subunit(s) led usually to a higher sensitivity to stress. In Arabidopsis thaliana genome, there are five genes encoding NACα subunit, and two genes encoding NACβ. Double homozygous mutant in both genes coding for NACβ was acquired, which showed a delayed development compared to the wild type, had abnormal number of flower organs, shorter siliques and greatly reduced seed set. Both NACβ genes were characterized in more detail-the phenotype of the double homozygous mutant was complemented by a functional NACβ copy. Then, both NACβ genes were localized to nuclei and cytoplasm and their promoters were active in many organs (leaves, cauline leaves, flowers, pollen grains, and siliques together with seeds). Since flowers were the most affected organs by nacβ mutation, the flower buds' transcriptome was identified by RNA sequencing, and their proteome by gel-free approach. The differential expression analyses of transcriptomic and proteomic datasets suggest the involvement of NACβ subunits in stress responses, male gametophyte development, and photosynthesis.

Worming into the Uncharacterized Human Proteome

Using neXtProt release 2019-01-11, we manually curated a list of 1837 functionally uncharacterized human proteins. Using OrthoList 2, we found that 270 of them have homologues in Caenorhabditis elegans, including 60 with a one-to-one orthology relationship. According to annotations extracted from WormBase, the vast majority of these 60 worm genes have RNAi experimental data or mutant alleles, but manual inspection shows that only 15% have phenotypes that could be interpreted in terms of a specific function. One third of the worm orthologs have protein-protein interaction data, and two of these interactions are conserved in humans. The combination of phenotypic, protein-protein interaction, and gene expression data provides functional hypotheses for 8 uncharacterized human proteins. Experimental validation in human or orthologs is necessary before they can be considered for annotation.

Dephosphorylation of the transcriptional cofactor NACA by the PP1A phosphatase enhances cJUN transcriptional activity and osteoblast differentiation

The transcriptional cofactor nascent polypeptide-associated complex and co-regulator α (NACA) regulates osteoblast maturation and activity. NACA functions, at least in part, by binding to Jun proto-oncogene, AP-1 transcription factor subunit (cJUN) and potentiating the transactivation of AP-1 targets such as osteocalcin (Bglap) and matrix metallopeptidase 9 (Mmp9). NACA activity is modulated by phosphorylation carried out by several kinases, but a phosphatase regulating NACA's activity remains to be identified. Here, we used affinity purification with MS in HEK293T cells to isolate NACA complexes and identified protein phosphatase 1 catalytic subunit α (PP1A) as a NACA-associated Ser/Thr phosphatase. NACA interacted with multiple components of the PP1A holoenzyme complex: the PPP1CA catalytic subunit and the regulatory subunits PPP1R9B, PPP1R12A and PPP1R18. MS analysis revealed that NACA co-expression with PPP1CA causes dephosphorylation of NACA at Thr-89, Ser-151, and Thr-174. NACA Ser/Thr-to-alanine variants displayed increased nuclear localization, and NACA dephosphorylation was associated with specific recruitment of novel NACA interactants, such as basic transcription factor 3 (BTF3) and its homolog BTF3L4. NACA and PP1A cooperatively potentiated cJUN transcriptional activity of the AP-1-responsive MMP9-luciferase reporter, which was abolished when Thr-89, Ser-151, or Thr-174 were substituted with phosphomimetic aspartate residues. We confirmed the NACA-PP1A interaction in MC3T3-E1 osteoblastic cells and observed that NACA phosphorylation status at PP1A-sensitive sites is important for the regulation of AP-1 pathway genes and for osteogenic differentiation and matrix mineralization. These results suggest that PP1A dephosphorylates NACA at specific residues, impacting cJUN transcriptional activity and osteoblast differentiation and function.

Lrp6 is a target of the PTH-activated αNAC transcriptional coregulator

In the nucleus of differentiated osteoblasts, the alpha chain of nascent polypeptide associated complex (αNAC) interacts with cJUN transcription factors to regulate the expression of target genes, including Osteocalcin (Bglap2). PTH induces the phosphorylation of αNAC on serine 99 through a Gαs-PKA dependent pathway. This leads to activation of αNAC and expression of Bglap2. To identify additional target genes regulated by PTH-activated αNAC, we performed ChIP-Seq against αNAC in PTH-treated MC3T3-E1 cells. This identified Low density lipoprotein receptor-Related Protein 6 (Lrp6) as a potential αNAC target. LRP6 acts as a co-receptor for the PTH receptor to allow optimal activation of PTH signaling. PTH increased Lrp6 mRNA levels in primary osteoblasts. Conventional quantitative ChIP confirmed the ChIP-Seq results. To assess whether αNAC plays a critical role in PTH-stimulated Lrp6 expression, we knocked-down Naca expression in MC3T3-E1 cells. Reduction of αNAC levels decreased basal expression of Lrp6 by 30% and blocked the stimulation of Lrp6 expression by PTH. We cloned the proximal mouse Lrp6 promoter (-2523/+120 bp) upstream of the luciferase reporter. Deletion and point mutations analysis in electrophoretic mobility shift assays and transient transfections identified a functional αNAC binding site centered around -343 bp. ChIP and ChIP-reChIP against JUND and αNAC showed that they cohabit on the proximal Lrp6 promoter. Luciferase assays confirmed that PTH-activated αNAC potentiated JUND-mediated Lrp6 transcription and Jund knockdown abolished this response. This study identified a novel αNAC target gene induced downstream of PTH signaling and represents the first characterization of the regulation of Lrp6 transcription in osteoblasts.

Quantitative proteome-level analysis of paulownia witches' broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes

Paulownia witches' broom (PaWB) disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ) to quantify and analyze the proteome-level changes among healthy P. fortunei (PF), PaWB-infected P. fortunei (PFI), and PaWB-infected P. fortunei treated with 20 mg L^-1 or 60 mg L^-1 methyl methane sulfonate (MMS) (PFI-20 and PFI-60, respectively). A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process) and PFI-20 vs. PFI-60 (recovered process), and further found that many of the MMS-response proteins mapped to "photosynthesis" and "ribosome" pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1) carbohydrate and energy metabolism, (2) protein synthesis and degradation, and (3) stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.

A Proteomics Approach to Investigate miR-153-3p and miR-205-5p Targets in Neuroblastoma Cells

MicroRNAs are key regulators associated with numerous diseases. In HEK293 cells, miR-153-3p and miR-205-5p down-regulate alpha-synuclein (SNCA) and Leucine-rich repeat kinase 2 (LRRK2), two key proteins involved in Parkinson’s disease (PD). We have used two-dimensional gel electrophoresis (2D-PAGE) coupled to mass spectrometry (MS) to identify a spectrum of miR-153-3p and miR-205-5p targets in neuronal SH-SY5Y cells. We overexpressed and inhibited both microRNAs in SH-SY5Y cells and through comparative proteomics profiling we quantified ~240 protein spots from each analysis. Combined, thirty-three protein spots were identified showing significant (p-value < 0.05) changes in abundance. Modulation of miR-153-3p resulted in seven up-regulated proteins and eight down-regulated proteins. miR-205 modulation resulted in twelve up-regulated proteins and six down-regulated proteins. Several of the proteins are associated with neuronal processes, including peroxiredoxin-2 and -4, cofilin-1, prefoldin 2, alpha-enolase, human nucleoside diphosphate kinase B (Nm23) and 14-3-3 protein epsilon. Many of the differentially expressed proteins are involved in diverse pathways including metabolism, neurotrophin signaling, actin cytoskeletal regulation, HIF-1 signaling and the proteasome indicating that miR-153-3p and miR-205-5p are involved in the regulation of a wide variety of biological processes in neuroblastoma cells.

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.

Proteomic and metabolomic profiling of Valencia orange fruit after natural frost exposure

The aim of this study was to evaluate the response of orange fruit (Citrus sinensis var. Valencia Late) to freezing stress in planta, both immediately after the natural event and after a week, in order to understand the biochemical and molecular basis of the changes that later derive in internal and external damage symptoms. Using two-dimensional differential gel electrophoresis to analyze exposed and non-exposed fruit, 27 differential protein spots were detected in juice sacs and flavedo, among all comparisons made. Also, primary and secondary metabolites relative contents were analyzed in both tissues by gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry, respectively. Proteins and compounds involved in regulatory functions, iron metabolism, oxidative damage and carbohydrate metabolism were the most affected. Interestingly, three glycolytic enzymes were induced by cold, and there was an increase in fermentation products (volatiles); all of that suggests that more energy generation might be required from glycolysis to counter the cold stress. Moreover, a notable increase in sugar levels was observed after frost, but it was not at the expense of organic acids utilization. Consequently, these results suggest a probable redistribution of photoassimilates in the frost-exposed plants, tending to restore the homeostasis altered by that severe type of stress. Isosinensetin was the most cold-sensitive secondary metabolite because it could not be detected at all after the frost, constituting a possible tool to early diagnose freezing damage.

αNAC inhibition of the FADD-JNK axis plays anti-apoptotic role in multiple cancer cells

Nascent polypeptide-associated complex α (αNAC) is reportedly overexpressed in several types of cancers and regulates cell apoptosis under hypoxic conditions in HeLa cells. The aim of our study was to investigate the apoptotic function of αNAC in cancer progression. First, we observed the cellular effects of αNAC depletion. Mouse αNAC was used to restore the protein level and verify the effect. An Annexin V assay, a caspase activity reporter assay, an apoptotic molecular marker, and a colony formation assay were used as markers to investigate the mechanisms of cell death caused by αNAC depletion. The Cancer 10-pathway reporter assay was used to screen downstream pathways. PCR site-directed deletion based on the functional domains of αNAC was used to construct deletion mutants. Those functional domain deletion mutants were used to recover the apoptotic phenotype caused by αNAC depletion. Finally, the role of αNAC in TNF-related apoptosis-inducing ligand (TRAIL) treatment was investigated in vitro. We found that depletion of αNAC in multiple types of cancer cells induce typical apoptotic cell death. This anti-apoptotic function is mediated by the FADD/c-Jun N-terminal kinase pathway. Intact αNAC is required for the direct binding of FADD as well as its anti-apoptosis function. Either αNAC depletion or the deletion of the ubiquitin-associated domain of αNAC sensitizes L929 cancer cells to mTRAIL treatment. Our study revealed a αNAC anti-apoptotic function in multiple types of cancer cells and suggested its potential in cancer therapy.

Cytokine effects induced by the human autoallergen α-NAC

Autoallergy is a phenomenon found in a subgroup of patients with atopic dermatitis (AD). These patients exhibit serum IgE reactivity toward autoantigens like the alpha-chain of the nascent polypeptide-associated complex (α-NAC; Hom s 2). α-NAC has been shown before to induce T-cell proliferation and secretion of IFN-γ. To elucidate the immune modulating functions α-NAC may exert, we analyzed its effects on cytokine transcription and secretion in peripheral blood mononuclear cells (PBMCs), monocytes, and CD4+ T cells. Transcription and secretion of IFN-γ, IL-17, and IL-22 were increased in α-NAC-stimulated PBMCs. As IL-17 was significantly upregulated by α-NAC, we assessed signal transduction in PBMCs and found signal transducer and activator of transcription 3 phosphorylation in α-NAC-stimulated cells. Furthermore, we could show the importance of monocyte activation by α-NAC, as isolated T cells reacted only weakly toward the stimulation. Inhibition of IL-23 p19 led to lower amounts of IL-17 in the PBMC supernatants after α-NAC stimulation. α-NAC stimulation of PBMCs from non-allergic donors resulted in secretion of IL-10, which was greatly reduced in PBMCs from α-NAC-sensitized AD patients. Our findings provide insights into the mechanisms of autoallergy, investigating the interplay of immune cells, signaling events, and cytokines, which are known to be relevant in atopic skin inflammation.

An inducible expression system to measure rhodopsin transport in transgenic Xenopus rod outer segments

We developed an inducible transgene expression system in Xenopus rod photoreceptors. Using a transgene containing mCherry fused to the carboxyl terminus of rhodopsin (Rho-mCherry), we characterized the displacement of rhodopsin (Rho) from the base to the tip of rod outer segment (OS) membranes. Quantitative confocal imaging of live rods showed very tight regulation of Rho-mCherry expression, with undetectable expression in the absence of dexamethasone (Dex) and an average of 16.5 µM of Rho-mCherry peak concentration after induction for several days (equivalent to >150-fold increase). Using repetitive inductions, we found the axial rate of disk displacement to be 1.0 µm/day for tadpoles at 20 °C in a 12 h dark /12 h light lighting cycle. The average distance to peak following Dex addition was 3.2 µm, which is equivalent to ~3 days. Rods treated for longer times showed more variable expression patterns, with most showing a reduction in Rho-mCherry concentration after 3 days. Using a simple model, we find that stochastic variation in transgene expression can account for the shape of the induction response.

The nascent polypeptide-associated complex is a key regulator of proteostasis

The adaptation of protein synthesis to environmental and physiological challenges is essential for cell viability. Here, we show that translation is tightly linked to the protein-folding environment of the cell through the functional properties of the ribosome bound chaperone NAC (nascent polypeptide-associated complex). Under non-stress conditions, NAC associates with ribosomes to promote translation and protein folding. When proteostasis is imbalanced, NAC relocalizes from a ribosome-associated state to protein aggregates in its role as a chaperone. This results in a functional depletion of NAC from the ribosome that diminishes translational capacity and the flux of nascent proteins. Depletion of NAC from polysomes and re-localisation to protein aggregates is observed during ageing, in response to heat shock and upon expression of the highly aggregation-prone polyglutamine-expansion proteins and Aβ-peptide. These results demonstrate that NAC has a central role as a proteostasis sensor to provide the cell with a regulatory feedback mechanism in which translational activity is also controlled by the folding state of the cellular proteome and the cellular response to stress.

African swine fever virus controls the host transcription and cellular machinery of protein synthesis

Throughout a viral infection, the infected cell reprograms the gene expression pattern in order to establish a satisfactory antiviral response. African swine fever virus (ASFV), like other complex DNA viruses, sets up a number of strategies to evade the host's defense systems, such as apoptosis, inflammation and immune responses. The capability of the virus to persist in its natural hosts and in domestic pigs, which recover from infection with less virulent isolates, suggests that the virus displays effective mechanisms to escape host defense systems. ASFV has been described to regulate the activation of several transcription factors, thus regulating the activation of specific target genes during ASFV infection. Whereas some reports have concerned about anti-apoptotic ASFV genes and the molecular mechanisms by which ASFV interferes with inducible gene transcription and immune evasion, less is yet known regarding how ASFV regulates the translational machinery in infected cells, although a recent report has shown a mechanism for favored expression of viral genes based on compartmentalization of viral mRNA and ribosomes with cellular translation factors within the virus factory. The viral mechanisms involved both in the regulation of host genes transcription and in the control of cellular protein synthesis are summarized in this review.

αNAC interacts with histone deacetylase corepressors to control Myogenin and Osteocalcin gene expression

In the nucleus of differentiated osteoblasts, the DNA-binding αNAC protein acts as a transcriptional coactivator of the Osteocalcin gene. Chromatin immunoprecipitation-microarray assays (ChIP-chip) showed that αNAC binds the Osteocalcin promoter but also identified the Myogenin promoter as an αNAC target. Here, we confirm these array data using quantitative ChIP and further detected that αNAC binds to these promoters in myoblasts. Since these genes are differentially regulated during osteoblastogenesis or myogenesis, these results suggest cell- and promoter-context specific functions for αNAC. We hypothesized that αNAC dynamically recruits corepressors to inhibit Myogenin expression in cells committing to the osteoblastic lineage or to inhibit Osteocalcin transcription in differentiating myoblasts. Using co-immunoprecipitation assays, we detected complexes between αNAC and the corepressors HDAC1 and HDAC3, in myoblasts and osteoblasts. Sequential ChIP confirmed HDAC1 recruitment by αNAC at the Osteocalcin and Myogenin promoters. Interaction with the corepressors was detectable in pre-osteoblasts and in myoblasts but disappeared as the cells differentiate. Treatment with an HDAC inhibitor caused de-repression of Osteocalcin expression in myoblasts. Overexpression of αNAC in myoblasts inhibits expression of Myogenin and differentiation. However, overexpression of an N-terminus truncated αNAC mutant allowed myoblasts to express Myogenin and differentiate, and this mutant did not interact with HDAC1 or HDAC3. This study identified an additional DNA-binding target and novel protein-protein interactions for αNAC. We propose that αNAC plays a role in regulating gene transcription during mesenchymal cell differentiation by differentially recruiting corepressors at target promoters.

Unfolding of the C-terminal domain of the J-protein Zuo1 releases autoinhibition and activates Pdr1-dependent transcription

The C-terminal 69 residues of the J-protein Zuo1 are sufficient to activate Pdr1, a transcription factor involved in both pleiotropic drug resistance and growth control. Little is understood about the pathway of activation by this primarily ribosome associated Hsp40 co-chaperone. Here, we report that only the C-terminal 13 residues of Zuo1 are required for activation of Pdr1, with hydrophobic residues being critical for activity. Two-hybrid interaction experiments suggest that the interaction between this 13-residue Zuo1 peptide and Pdr1 is direct, analogous to the activation of Pdr1 by xenobiotics. However, simply dissociation of Zuo1 from the ribosome is not sufficient for induction of Pdr1 transcriptional activity, as the C-terminal 86 residues of Zuo1 fold into an autoinhibitory left-handed four-helix bundle. Hydrophobic residues critical for interaction with Pdr1 are sequestered within the structure of this C-terminal domain (CTD), necessitating unfolding for activation. Thus, although expression of the CTD does not result in activation, alterations that destabilize the structure cause induction of pleiotropic drug resistance. These destabilizing alterations also result in dissociation of the full-length protein from the ribosome. Thus, our results are consistent with an activation pathway in which unfolding of Zuo1's C-terminal helical bundle domain results in ribosome dissociation followed by activation of Pdr1 via a direct interaction.

EGD1 (β-NAC) mRNA is localized in a novel cytoplasmic structure in Saccharomyces cerevisiae

RNA localization is a common mechanism for recruiting proteins to specific regions of a cell, which causes cell polarization and sometimes asymmetric division. We found that EGD1 mRNA accumulates dose-dependently as a cytoplasmic granule in Saccharomyces cerevisiae. EGD1 encodes a β-subunit of the nascent polypeptide-associated complex (NAC). NAC is a heterodimer consisting of α- and β-subunits, associated with ribosomes and thought to be involved in the folding of nascent polypeptide chains. Analysis of deletion constructs showed that the localization of EGD1 mRNA requires both an upstream region and an ORF of EGD1, suggesting that the translation of Egd1p is important for localization. We also showed that Egd1p and P-body components are co-localized with EGD1 mRNA. This granule, named the EGD1 granule, has features similar to cellular inclusions containing aggregated proteins. Disruption of microtubules by treatment with a drug, benomyl, resulted in loss of the EGD1 granule. When the expression level of EGD2 encoding the αNAC increased, the percentage of cells showing the EGD1 granule decreased, suggesting that the granular distribution of EGD1 depends on the quantitative balance between α- and β-subunits of NAC. Taken together, we propose a novel microtubule-dependent mechanism for controlling NAC through RNA localization.

Temporal proteomic analysis of IGF-1R signalling in MCF-7 breast adenocarcinoma cells

Dysregulation of the insulin-like growth factor 1 receptor signalling network is implicated in tumour growth and resistance to chemotherapy. We explored proteomic changes resulting from insulin-like growth factor 1 stimulation of MCF-7 adenocarcinoma cells as a function of time. Quantitative analysis using iTRAQ reagents and 2-D LC-MS/MS analysis of three biological replicates resulted in the identification of 899 proteins (p<or=0.05) with an estimated mean false-positive rate of 2.6%. Quantitative protein expression was obtained from 681 proteins. Further analysis by supervised k-means clustering identified five temporal clusters, which were submitted to the FuncAssociate server to assign overrepresented gene ontology terms. Proteins associated with vesicle transport were significantly overrepresented. We further analyzed our data set for proteins showing temporal significance using the software, extraction and analysis of differential gene expression, resulting in 20 significantly and temporally changing proteins (p<or=0.1). These significant proteins play roles in, among others, altered glucose metabolism (lactate dehydrogenase A and pyruvate kinase M1/M2) and cellular stress (nascent polypeptide-associated complex subunit alpha and heat shock (HSC70) proteins). We used multiple reaction monitoring to validate these interesting proteins and have revealed several differences in relative peptide expression corresponding to protein isoforms and variants.

The crystal structure of the human nascent polypeptide-associated complex domain reveals a nucleic acid-binding region on the NACA subunit

In archaea and eukaryotes, the nascent polypeptide-associated complex (NAC) is one of the cytosolic chaperones that contact the nascent polypeptide chains as they emerge from the ribosome and assist in post-translational processes. The eukaryotic NAC is a heterodimer, and its two subunits form a stable complex through a dimerizing domain called the NAC domain. In addition to acting as a protein translation chaperone, the NAC subunits also function individually in transcriptional regulation. Here we report the crystal structure of the human NAC domain, which reveals the manner of human NAC dimerization. On the basis of the structure, we identified a region in the NAC domain of the human NAC alpha-subunit as a new nucleic acid-binding region, which is blocked from binding nucleic acids in the heterodimeric complex by a helix region in the beta-subunit.

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.

Nuclear alpha NAC influences bone matrix mineralization and osteoblast maturation in vivo

Nascent-polypeptide-associated complex and coactivator alpha (alpha NAC) is a protein shuttling between the nucleus and the cytoplasm. Upon phosphorylation at residue serine 43 by integrin-linked kinase, alpha NAC is translocated to the nuclei of osteoblasts, where it acts as an AP-1 coactivator to increase osteocalcin gene transcription. To determine the physiological role of nuclear alpha NAC, we engineered a knock-in mouse model with a serine-to-alanine mutation at position 43 (S43A). The S43A mutation resulted in a decrease in the amount of nuclear alpha NAC with reduced osteocalcin gene promoter occupancy, leading to a significant decrease in osteocalcin gene transcription. The S43A mutant bones also expressed decreased levels of alpha(1)(I) collagen mRNA and as a consequence had significantly less osteoid tissue. Transient transfection assays and chromatin immunoprecipitation confirmed the alpha(1)(I) collagen gene as a novel alpha NAC target. The reduced quantity of bone matrix in S43A mutant bones was mineralized faster, as demonstrated by the significantly reduced mineralization lag time, producing a lower volume of immature, woven-type bone characterized by poor lamellation and an increase in the number of osteocytes. Accordingly, the expression of the osteocyte differentiation marker genes DMP-1 (dentin matrix protein 1), E11, and SOST (sclerostin) was increased. The accelerated mineralization phenotype was cell autonomous, as osteoblasts isolated from the calvaria of S43A mutant mice mineralized their matrix faster than did wild-type cells. Thus, inhibition of alpha NAC nuclear translocation results in an osteopenic phenotype caused by reduced expression of osteocalcin and type I collagen, accelerated mineralization, and immature woven-bone formation.

alphaNAC depletion as an initiator of ER stress-induced apoptosis in hypoxia

Accumulation of unfolded proteins triggers endoplasmic reticulum (ER) stress and is considered a part of the cellular responses to hypoxia. The nascent polypeptide-associated complex (NAC) participates in the proper maturation of newly synthesized proteins. However, thus far, there have been no comprehensive studies on NAC involvement in hypoxic stress. Here, we show that hypoxia activates glycogen synthase kinase-3beta (GSK-3beta) and that the activated GSK-3beta destabilizes alphaNAC with the subsequent apoptosis of the cell. Hypoxia of various cell types and the mouse ischemic brain was associated with rapid downregulation of alphaNAC and ER stress responses involving PERK, ATF4, gamma-taxilin, elF2alpha, Bip, and CHOP. Depletion of alphaNAC by RNA interference specifically activated ER stress responses and caused mitochondrial dysfunction, which resulted in apoptosis through caspase activation. Interestingly, we found that the hypoxic conditions activated GSK-3beta, and that GSK-3beta inhibition prevented alphaNAC protein downregulation in hypoxic cells and rescued the cells from apoptosis. In addition, alphaNAC overexpression increased the viability of hypoxic cells. Taken together, these results suggest that alphaNAC degradation triggers ER stress responses and initiates apoptotic processes in hypoxic cells, and that GSK-3beta may participate upstream in this mechanism.

Proteomic identification of differently expressed proteins responsible for osteoblast differentiation from human mesenchymal stem cells

Human mesenchymal stem cells (hMSC) are a population of multipotent cells that can differentiate into osteoblasts, chondrocytes, adipocytes, and other cells. The exact mechanism governing the differentiation of hMSC into osteoblasts remains largely unknown. Here, we analyzed protein expression profiles of undifferentiated as well as osteogenic induced hMSC using 2-D gel electrophoresis (2-DE), mass spectrometry (MS), and peptide mass fingerprinting (PMF) to investigate the early gene expression in osteoblast differentiation. We have generated proteome maps of undifferentiated hMSC and osteogenic induced hMSC on day 3 and day 7. 2-DE revealed 102 spots with at least 2.0-fold changes in expression and 52 differently expressed proteins were successfully identified by MALDI-TOF-MS. These proteins were classified into 7 functional categories: metabolism, signal transduction, transcription, calcium-binding protein, protein degradation, protein folding and others. The expression of some identified proteins was confirmed by further RT-PCR analyses. This study clarifies the global proteome during osteoblast differentiation. Our results will play an important role in better elucidating the underlying molecular mechanism in hMSC differentiation into osteoblasts.

Thoracic skeletal defects and cardiac malformations: a common epigenetic link?

Congenital heart defects (CHDs) are the most common birth defects in humans. In addition, cardiac malformations represent the most frequently identified anomaly in teratogenicity experiments with laboratory animals. To explore the mechanisms of these drug-induced defects, we developed a model in which pregnant rats are treated with dimethadione, resulting in a high incidence of heart malformations. Interestingly, these heart defects were accompanied by thoracic skeletal malformations (cleft sternum, fused ribs, extra or missing ribs, and/or wavy ribs), which are characteristic of anterior-posterior (A/P) homeotic transformations and/or disruptions at one or more stages in somite development. A review of other teratogenicity studies suggests that the co-occurrence of these two disparate malformations is not unique to dimethadione, rather it may be a more general phenomenon caused by various structurally unrelated agents. The coexistence of cardiac and thoracic skeletal malformations has also presented clinically, suggesting a mechanistic link between cardiogenesis and skeletal development. Evidence from genetically modified mice reveals that several genes are common to heart development and to formation of the axial skeleton. Some of these genes are important in regulating chromatin architecture, while others are tightly controlled by chromatin-modifying proteins. This review focuses on the role of these epigenetic factors in development of the heart and axial skeleton, and examines the hypothesis that posttranslational modifications of core histones may be altered by some developmental toxicants.

Differential mechanisms of transcriptional regulation of the mouse osteocalcin gene by Jun family members

The osteocalcin gene encodes an osteoblast-specific protein that is induced with the onset of mineralization at late stages of differentiation. Several transcriptional regulators have been characterized that control the transcription of osteocalcin, including activator protein 1 (AP-1) family members such as the Fra2/JunD heterodimer. We have previously shown that the c-Jun homodimer activates transcription from the murine osteocalcin proximal promoter and that this response is potentiated by the alpha chain of the nascent polypeptide-associated complex (alphaNAC) transcriptional coactivator. We now further explore the mechanisms involved and show that c-Jun binds two cryptic AP-1 sites within the proximal promoter of osteocalcin and that this binding is strictly alphaNAC-dependent. Chromatin immunoprecipitation (ChIP) confirmed that c-Jun occupies its binding sites within the osteocalcin 5'-flanking region in living osteoblasts. Interestingly, the ChIP assay revealed that both JunB and JunD also bind the osteocalcin promoter. JunD, but not JunB, stimulated osteocalcin gene transcription in transient transfection assays, but this effect was not potentiated by alphaNAC. Thus, the c-Jun and JunD family members utilize distinct mechanisms that implicate differential interaction with transcriptional coactivators to regulate osteocalcin expression.

Characterisation of the nascent polypeptide-associated complex in fission yeast

The nascent polypeptide-associated complex (NAC) is an abundant and phylogenetically conserved protein complex. It is composed of two subunits and interacts with nascent polypeptide chains emerging from the ribosome. It has been proposed to protect the nascent chains from premature interaction with other cell proteins, but has also been found to associate with DNA junctions, and to be involved in other processes including transcription regulation and mitochondrial protein import.Here, we characterize NAC in fission yeast. We find that NAC is associated with ribosomes, while a significant fraction remains in a free form. The NAC alpha subunit contains a ubiquitin-associated (UBA) domain, which is found in several proteins involved in the ubiquitin-proteasome pathway for protein degradation. However, NAC does not associate with ubiquitin chains and mutants lacking NAC did not exhibit any obvious defects in protein degradation. Accordingly, we find that the NAC UBA domain belongs to an ancient and distinct subgroup of the UBA family. In contrast to the situation with budding yeast, fission yeast cells devoid of NAC were not temperature sensitive. However, they displayed resistance to the amino acid analogue canavanine, in accordance with the idea that NAC is involved in protein quality control.

Comparative proteomic analysis of NaCl stress-responsive proteins in Arabidopsis roots

NaCl stress is a major abiotic stress limiting the productivity and the geographical distribution of many plant species. Roots are the primary site of salinity perception. To understand better NaCl stress responses in Arabidopsis roots, a comparative proteomic analysis of roots that had been exposed to 150 mM NaCl for either 6 h or 48 h was conducted. Changes in the abundance of protein species within roots were examined using two-dimensional electrophoresis. Among the >1000 protein spots reproducibly detected on each gel, the abundance of 112 protein spots decreased and 103 increased, at one or both time points, in response to NaCl treatment. Through liquid-chromatography-tandem mass spectrometry, identity was assigned to 86 of the differentially abundant spots. The proteins identified included many previously characterized stress-responsive proteins and others related to processes including scavenging for reactive oxygen species; signal transduction; translation, cell wall biosynthesis, protein translation, processing and degradation; and metabolism of energy, amino acids, and hormones. At the resolution of individual genes and proteins, poor statistical correlation (6 h, r= -0.13; 48 h, r=0.11) of these protein expression data with previous microarray results was detected, supporting the concept that post-transcriptional regulation plays an important role in stress-responsive gene expression, and highlighting the need for combined transcriptomic and proteomic analyses.

A comparative proteome and phosphoproteome analysis of differentially regulated proteins during fertilization in the self-incompatible speciesSolanum chacoense Bitt

We have used 2-DE for a time-course study of the changes in protein and phosphoprotein expression that occur immediately after fertilization in Solanum chacoense. The phosphorylation status of the detected proteins was determined with three methods: in vivo labeling, immunodetection, and phosphoprotein-specific staining. Using a pI range of 4-7, 262 phosphorylated proteins could be mapped to the 619 proteins detected by Sypro Ruby staining, representing 42% of the total proteins. Among these phosphoproteins, antibodies detected 184 proteins from which 78 were also detected with either of the other two methods (42%). Pro-Q Diamond phosphoprotein stain detected 111 proteins, of which 76 were also detected with either of the other two methods (68%). The 32P in vivo labeling method detected 90 spots from which 78 were also detected with either of other two methods (87%). On comparing before and after fertilization profiles, 38 proteins and phosphoproteins presented a reproducible change in their accumulation profiles. Among these, 24 spots were selected and analyzed by LC-MS/MS using a hybrid quadrupole-TOF (Q-TOF) instrument. Peptide data were searched against publicly available protein and EST databases, and the putative roles of the identified proteins in early fertilization events are discussed.

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.

Inhibition of ATF4 transcriptional activity by FIAT/gamma-taxilin modulates bone mass accrual

The basic domain-leucine zipper protein, activating transcription factor 4 (ATF4), was recently shown to control key aspects of osteoblast biology. ATF4 regulates the timely onset of osteoblast differentiation, the synthesis of type I collagen, and the transcription of the osteocalcin and RANKL (receptor activator of NFkappa-B ligand) genes. Accordingly, the levels and activity of ATF4 are under tight control through mechanisms that include protein stability and phosphorylation. We have uncovered yet another mode of inhibition of ATF4 through its interaction with the leucine zipper protein FIAT (Factor Inhibiting ATF4-mediated Transcription, also described as gamma-taxilin). FIAT/gamma-taxilin localizes to the nucleus in osteoblasts and dimerizes with ATF4 to form inactive dimers, because it does not contain a DNA-binding basic domain moiety. The interaction of FIAT/gamma-taxilin with ATF4 thus inhibits ATF4-mediated transcription. Transgenic mice overexpressing FIAT/gamma-taxilin show osteopenia and reduced expression of the ATF4 target gene, osteocalcin. Interestingly, FIAT/gamma-taxilin also interacts with the transcriptional co-activator alphaNAC (Nascent polypeptide associated complex And Coactivator alpha), suggesting alternative, non-mutually exclusive mechanisms contributing to the inhibition of ATF4-dependent osteocalcin gene transcription by FIAT/gamma-taxilin.

Proteomic analysis of salt stress-responsive proteins in rice root

Salt stress is one of the major abiotic stresses in agriculture worldwide. We report here a systematic proteomic approach to investigate the salt stress-responsive proteins in rice (Oryza sativa L. cv. Nipponbare). Three-week-old seedlings were treated with 150 mM NaCl for 24, 48 and 72 h. Total proteins of roots were extracted and separated by two-dimensional gel electrophoresis. More than 1100 protein spots were reproducibly detected, including 34 that were up-regulated and 20 down-regulated. Mass spectrometry analysis and database searching helped us to identify 12 spots representing 10 different proteins. Three spots were identified as the same protein, enolase. While four of them were previously confirmed as salt stress-responsive proteins, six are novel ones, i.e. UDP-glucose pyrophosphorylase, cytochrome c oxidase subunit 6b-1, glutamine synthetase root isozyme, putative nascent polypeptide associated complex alpha chain, putative splicing factor-like protein and putative actin-binding protein. These proteins are involved in regulation of carbohydrate, nitrogen and energy metabolism, reactive oxygen species scavenging, mRNA and protein processing, and cytoskeleton stability. This study gives new insights into salt stress response in rice roots and demonstrates the power of the proteomic approach in plant biology studies.

FIAT represses ATF4-mediated transcription to regulate bone mass in transgenic mice

We report the characterization of factor inhibiting activating transcription factor 4 (ATF4)–mediated transcription (FIAT), a leucine zipper nuclear protein. FIAT interacted with ATF4 to inhibit binding of ATF4 to DNA and block ATF4-mediated transcription of the osteocalcin gene in vitro. Transgenic mice overexpressing FIAT in osteoblasts also had reduced osteocalcin gene expression and decreased bone mineral density, bone volume, mineralized volume, trabecular thickness, trabecular number, and decreased rigidity of long bones. Mineral homeostasis, osteoclast number and activity, and osteoblast proliferation and apoptosis were unchanged in transgenics. Expression of osteoblastic differentiation markers was largely unaffected and type I collagen synthesis was unchanged. Mineral apposition rate was reduced in transgenic mice, suggesting that the lowered bone mass was due to a decline in osteoblast activity. This cell-autonomous decrease in osteoblast activity was confirmed by measuring reduced alkaline phosphatase activity and mineralization in primary osteoblast cultures. These results show that FIAT regulates bone mass accrual and establish FIAT as a novel transcriptional regulator of osteoblastic function.

Sequence-specific DNA binding by the alphaNAC coactivator is required for potentiation of c-Jun-dependent transcription of the osteocalcin gene

Since the c-Jun coactivator alphaNAC was initially identified in a differential screen for genes expressed in differentiated osteoblasts, we examined whether the osteocalcin gene, a specific marker of terminal osteoblastic differentiation, could be a natural target for the coactivating function of alphaNAC. We had also previously shown that alphaNAC can specifically bind DNA in vitro, but it remained unclear whether the DNA-binding function of alphaNAC is expressed in vivo or if it is required for coactivation. We have identified an alphaNAC binding site within the murine osteocalcin gene proximal promoter region and demonstrated that recombinant alphaNAC or alphaNAC from ROS17/2.8 nuclear extracts can specifically bind this element. Using transient transfection assays, we have shown that alphaNAC specifically potentiated the c-Jun-dependent transcription of the osteocalcin promoter and that this activity specifically required the DNA-binding domain of alphaNAC. Chromatin immunoprecipitation confirmed that alphaNAC occupies its binding site on the osteocalcin promoter in living osteoblastic cells expressing osteocalcin. Inhibition of the expression of endogenous alphaNAC in osteoblastic cells by use of RNA interference provoked a decrease in osteocalcin gene transcription. Our results show that the osteocalcin gene is a target for the alphaNAC coactivating function, and we propose that alphaNAC is specifically targeted to the osteocalcin promoter through its DNA-binding activity as a means to achieve increased specificity in gene transcription.

NACA is a positive regulator of human erythroid-cell differentiation

We have previously identified the transcript encoding NACA (the α chain of the nascent-polypeptide-associated complex) as a cytokine-modulated specific transcript in the human TF-1 erythroleukemic cell line. This protein was already known to be a transcriptional co-activator that acts by potentiating AP-1 activity in osteoblasts, and is known to be involved in the targeting of nascent polypeptides. In this study, we investigate the role of NACA in human hematopoiesis.

Protein distribution analyses indicate that NACA is expressed in undifferentiated TF-1 cells and in human-cord-blood-derived CD34+ progenitor cells. Its expression is maintained during in vitro erythroid differentiation but, in marked contrast, its expression is suppressed during their megakaryocytic or granulocytic differentiation. Ectopic expression of NACA in CD34+ cells under culture conditions that induce erythroid-lineage differentiation leads to a marked acceleration of erythroid-cell differentiation. Moreover, ectopic expression of NACA induces erythropoietin-independent differentiation of TF-1 cells, whereas downregulation of NACA by RNA interference abolishes the induction of hemoglobin production in these cells and diminishes glycophorin-A (GPA) expression by CD34+ progenitors cultured under erythroid differentiation conditions. Altogether, these results characterize NACA as a new factor involved in the positive regulation of human erythroid-cell differentiation.

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.

Interaction of the taxilin family with the nascent polypeptide-associated complex that is involved in the transcriptional and translational processes

alpha-Taxilin is a novel binding partner of the syntaxin family, which is implicated in intracellular vesicle traffic. We have here found that alpha-taxilin interacts with the nascent polypeptide-associated complex (NAC), which is involved in transferring growing nascent polypeptide chains to appropriate co-translationally acting factors. NAC is composed of two subunits, alpha- and betaNACs. Both these subunits bound to alpha-taxilin through its C-terminal coiled-coil region in dose-dependent and saturable manners. The interactions of alpha-taxilin with alphaNAC and NAC but not with betaNAC were inhibited by syntaxin-4, indicating that alpha-taxilin binds to NAC mainly through its interaction with alphaNAC. When alphaNAC was over-expressed in COS-7 cells, alphaNAC was distributed in the cytosol and nucleus. However, co-expression of the alpha-taxilin fragment containing the alphaNAC-binding region eliminated the nuclear distribution of over-expressed alphaNAC. Moreover, other taxilin family members, beta- and gamma-taxilins, also bound to alphaNAC and thereby affected the nuclear distribution of over-expressed alphaNAC. Taken together with the evidence that alphaNAC functions in the nucleus as a transcriptional coactivator, our results raise the possibility that the taxilin family is involved not only in the translational process through its interaction with NAC but also in the transcriptional process through its interaction with alphaNAC alone.

Casein kinase II phosphorylation regulates alphaNAC subcellular localization and transcriptional coactivating activity

The subcellular localization of the alphaNAC coactivator is regulated, but the signaling pathways controlling its nucleocytoplasmic shuttling and coactivation function are not completely characterized. We report here that casein kinase II (CK2) phosphorylated alphaNAC on several phosphoacceptor sites, especially in an amino-terminal cluster. Deletion or mutation of the clustered CK2 sites induced nuclear accumulation of alphaNAC in cells. alphaNAC also localized to the nucleus when endogenous CK2 activity was inhibited by quercetin or 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). These observations suggested that phosphorylation by CK2 might play a signaling role in the nuclear export of alphaNAC. Interestingly, inhibition of the chromosome region maintenance 1 (CRM1) exportin by leptomycin B (LMB) led to accumulation of alphaNAC in the nucleus. We conclude that CK2 phosphorylation of the N-terminal cluster corresponds to the signal for alphaNAC's nuclear export via a CRM1-dependent pathway. Finally, the nuclear accumulation of the protein resulting from the lack of CK2 phosphorylation mediated a slight but significant increase of the alphaNAC coactivating function on AP-1 transcriptional activity. Thus, alphaNAC's exit from the nucleus and capacity to potentiate transcription appear dependent on its phosphorylation status.

Integrin-linked Kinase Regulates the Nuclear Entry of the c-Jun Coactivator α-NAC and Its Coactivation Potency

Overexpression of the integrin-linked kinase (ILK) was shown to increase c-Jun-dependent transcription. We now show that this effect of ILK involves the c-Jun transcriptional coactivator, nascent polypeptide-associated complex and coactivator alpha (alpha-NAC). ILK phosphorylated alpha-NAC on residue Ser-43 upon adhesion of cells to fibronectin. Co-expression of constitutively active ILK with alpha-NAC led to the nuclear accumulation of the coactivator. Conversely, alpha-NAC remained in the cytoplasm of cells transfected with a dominant-negative ILK mutant, and a mutated alpha-NAC at phosphoacceptor position Ser-43 (S43A) also localized outside of the nucleus. The S43A alpha-NAC mutant could not potentiate the effect of ILK on c-Jun-dependent transcription. We conclude that ILK-dependent phosphorylation of alpha-NAC induced the nuclear accumulation of the coactivator and that phosphorylation of alpha-NAC by ILK is required for the potentiation of c-Jun-mediated responses by the kinase. The results represent one of the rare examples of a transcriptional coactivator shuttling between the cytosol and the nucleus.

African swine fever virus proteins involved in evading host defence systems

African swine fever virus (ASFV) can cause an acutely fatal haemorrhagic fever in domestic pigs although in its natural hosts, warthogs, bushpigs and the soft tick vector, Ornithodoros moubata, ASFV causes inapparent persistent infections. The virus is a large, cytoplasmic, double-stranded DNA virus which has a tropism for macrophages. As it is the only member of the Asfarviridae family, ASFV encodes many novel genes not encoded by other virus families. The ability of the virus to persist in its natural hosts and in domestic pigs, which recover from infection with less virulent isolates, shows that the virus has effective mechanisms to evade host defence systems. This review focuses on recent progress made in understanding the function of ASFV-encoded proteins, which are involved in modulating the host response to infection. Growing evidence suggests that a major strategy used by the virus is to modulate signalling pathways in infected macrophages, thus interfering with the expression of a large number of immunomodulatory genes. One potent immunomodulatory protein, A238L, inhibits both activation of the host NFkappaB transcription factor and inhibits calcineurin phosphatase activity. Calcineurin-dependent pathways, including activation of the NFAT transcription factor, are therefore inhibited. Another ASFV-encoded protein, CD2v, resembles the host CD2 protein, which is expressed on T cells and NK cells. This virus protein causes the adsorption of red blood cells around virus-infected cells and extracellular virus particles. Expression of the CD2v protein aids virus dissemination in pigs and the protein also has a role in impairing bystander lymphocyte function. This may be mediated either by a direct interaction of CD2v extracellular domain with ligands on lymphocytes or by an indirect mechanism involving interaction of the CD2v cytoplasmic tail with host proteins involved in signalling or trafficking pathways. Two ASFV proteins, an IAP and a Bcl2 homologue, inhibit apoptosis in infected cells and thus facilitate production of progeny virions. The prediction is that half to two-thirds of the approximately 150 genes encoded by ASFV are not essential for replication in cells but have an important role for virus survival and transmission in its hosts. These genes provide an untapped repository, and will be valuable tools for deciphering not only how the virus manipulates the host response to infection to avoid elimination, but also useful for understanding important host anti-viral mechanisms. In addition, they may provide leads for discovery of novel immunomodulatory drugs.