A Human Proteome Microarray Identifies that the Heterogeneous Nuclear Ribonucleoprotein K (hnRNP K) Recognizes the 5′ Terminal Sequence of the Hepatitis C Virus RNA

Stem-loop I (SL1) located in the 5′ untranslated region of the hepatitis C virus (HCV) genome initiates binding to miR-122, a microRNA required for hepatitis HCV replication. However, proteins that bind SL1 remain elusive. In this study, we employed a human proteome microarray, comprised of ∼17,000 individually purified human proteins in full-length, and identified 313 proteins that recognize HCV SL1. Eighty-three of the identified proteins were annotated as liver-expressing proteins, and twelve of which were known to be associated with hepatitis virus. siRNA-induced silencing of eight out of 12 candidate genes led to at least 25% decrease in HCV replication efficiency. In particular, knockdown of heterogeneous nuclear ribonucleoprotein K (hnRNP K) reduced HCV replication in a concentration-dependent manner. Ultra-violet-crosslinking assay also showed that hnRNP K, which functions in pre-mRNA processing and transport, showed the strongest binding to the HCV SL1. We observed that hnRNP K, a nuclear protein, is relocated in the cytoplasm in HCV-expressing cells. Immunoprecipitation of the hnRNP K from Huh7.5 cells stably expressing HCV replicon resulted in the co-immunoprecipitation of SL1. This work identifies a cellular protein that could have an important role in the regulation of HCV RNA gene expression and metabolism.RNA viruses are the cause of numerous human diseases. Because of their relatively simple genomes, successful infection by RNA viruses is intimately linked to host factors that can both contribute to, or antagonize the viral infection process (1–3). Infection by the hepatitis C virus (HCV)¹, a positive-sense RNA virus, can lead to liver cirrhosis and hepatocellular carcinoma. Approximately 2–3% of the world''s population is chronically infected with HCV, with more than 350,000 annual fatalities in recent years (4). As is typical for viruses, a large number of host factors have been reported to facilitate HCV infection including microRNA-122 (miR-122), CD81, claudin-1, cyclophilins, and lipoproteins, to name a few (5–9). These cellular factors interact with viral proteins or RNA, thus promoting HCV entry, genome translation, and replication.The 5′-untranslated region (5′-UTR) of the HCV RNA genome contains complex RNA structures that interact with cellular factors. These structures include the internal ribosomal entry site that regulates cap-independent translation of the viral RNA (10–11). The 5′-most stem-loop (SL) structure, namely SL1, has been reported to interact with miR-122 to increase the stability of the genomic RNA and facilitate HCV RNA replication in cells (12–13). However, host proteins that can bind to SL1 remain largely elusive because of a lack of proper tools. Previously, we have shown that functional protein microarrays, comprised of individually purified yeast proteins, are an ideal tool to identify proteins that directly interact with important RNA structures encoded by an RNA virus (14). Here, we took a similar approach using a human proteome microarray to identify human hnRNP K as a specific HCV SL1-binding protein that is required for efficient HCV RNA replication.     

Heterogeneous Nuclear Ribonucleoprotein K Represses the Production of Pro-apoptotic Bcl-xS Splice Isoform

The Bcl-x pre-mRNA is alternatively spliced to produce the anti-apoptotic Bcl-x_L and the pro-apoptotic Bcl-x_S isoforms. By performing deletion mutagenesis on a human Bcl-x minigene, we have identified a novel exonic element that controls the use of the 5′ splice site of Bcl-x_S. The proximal portion of this element acts as a repressor and is located downstream of an enhancer. Further mutational analysis provided a detailed topological map of the regulatory activities revealing a sharp transition between enhancer and repressor sequences. Portions of the enhancer can function when transplanted in another alternative splicing unit. Chromatography and immunoprecipitation assays indicate that the silencer element interacts with heterogeneous ribonucleoprotein particle (hnRNP) K, consistent with the presence of putative high affinity sites for this protein. Finally, down-regulation of hnRNP K by RNA interference enhanced splicing to Bcl-x_S, an effect seen only when the sequences bound by hnRNP K are present. Our results therefore document a clear role for hnRNP K in preventing the production of the pro-apoptotic Bcl-x_S splice isoform.Alternative splicing is a major mechanism used to augment the number of proteins encoded by the genome. It is estimated that as many as 97% of multiple exon pre-mRNAs undergo alternative splicing (1, 2). Disruption of alternative splicing by mutating important regulatory sequences or by altering the expression or activity of proteins controlling splice site selection has been linked with different diseases, including cancer (3–7). Apoptosis is an important and complex cellular program involved in development and differentiation in higher organisms (8, 9). However, its aberrant control often contributes to cancer development and the resistance of cancer cells to drug therapy (10–13).Genes implicated in the apoptotic pathway are alternatively spliced often to produce protein isoforms with distinct or even antagonistic activities (14, 15). A good example is the apoptotic regulator Bcl-x, which is alternatively spliced to produce two major isoforms, the anti-apoptotic Bcl-x_L protein and the shorter pro-apoptotic Bcl-x_S isoform (16). This alternative splicing decision involves a competition between two 5′ splice sites; the use of the downstream site creates Bcl-x_L, and the use of the upstream one produces Bcl-x_S (Fig. 1A). Bcl-x_L is always the predominant form in cancer cells, and overexpressing it can confer resistance to chemotherapeutic agents (17–22). On the other hand, overexpression of the pro-apoptotic Bcl-x_S isoform enhances sensitivity to the topoisomerase inhibitor etoposide and to taxol in a breast cancer cell line, while triggering apoptosis in melanoma cell lines (23, 24). Using antisense technologies to improve the production of the Bcl-x_S splice variant can also induce apoptosis in cancer cells (25–27).Open in a separate windowFIGURE 1.A, alternative splicing of Bcl-x produces two major isoforms, Bcl-x_L and Bcl-x_S. B, regulation of Bcl-x alternative splicing. The enhancer elements are shown as white boxes, and the repressors are black. The pointed and flat arrows indicate positive and negative regulation, respectively. Protein kinase C inhibition relieves repression caused by the SB1 element on the Bcl-x_S splice site (36). The repressor elements CRCE1, recognized by SAP155, and CRCE2 mediate the production of Bcl-x_S by ceramide as when induced by gemcitabine in A549 cells (38, 39). hnRNP F/H binds to the B2G element to enhance the production of the Bcl-x_S isoform (41). RBM25, through an element located upstream of the Bcl-x_S splice site, can also augment its use (44). A large intronic region (IRE) mediates the Bcl-x_L increase caused by interleukin-6 (IL-6), granulocyte-macrophage colony-stimulating factor (GM-CSF), and 12-O-tetradecanoylphorbol-13-acetate (TPA) (35). Finally, the B3 region also enhances Bcl-x_L formation through the binding of SRp30c to AM2 and ML2 and the U1 snRNP to two cryptic 5′ splice sites (42).Alternative splicing is regulated by different proteins bound to sequence elements near splice sites. A variety of mechanisms is used to achieve regulation. Some splicing factors act by recruiting or inhibiting the binding of different components of the spliceosome. Others may change the conformation of the pre-mRNA to mask a splice site or to bring a pair of splice sites into closer proximity (28, 29).Although individual factors can have a strong and specific effect on splicing decisions, alternative splicing often relies on a combination of factors to determine the appropriate levels of isoforms. The implication of multiple proteins likely provides additional levels of regulation that helps attuned splicing control to a variety of stresses, environmental cues, and growth conditions. In several cases, the interaction of regulatory factors can be antagonistic. For example, in the Drosophila male-specific-lethal-2 (msl-2) pre-mRNA, recruitment of SXL to a uridine-rich region interferes with the binding of TIA-1 that is necessary for efficient U1 snRNP² recruitment at the 5′ splice site (30). On the same pre-mRNA, SXL also diminishes U2AF recognition of the polypyrimidine tract at the 3′ splice site. TIA proteins bound to a U-rich element on the avian myosin phosphatase targeting subunit-1 (MYPT1) pre-mRNA repress the binding of PTB (31). PTB can also reduce the recruitment of ETR-3 to intronic elements near exon 5 of cardiac troponin T (32). In neurons, the binding of PTB to the introns surrounding the N1 exon of c-src is antagonized by nPTB protein, promoting exon inclusion. On the hnRNP A1 pre-mRNA, PTB diminishes the binding of SRp30c to the intronic CE9 element, reducing the inhibition by this protein on the use of the downstream 3′ splice site (33). SC35 and hnRNP A1 have partially overlapping binding sites on the human immunodeficiency virus 1 (HIV-1) tat exon 2. Preferential binding of SC35 enhances the inclusion of the exon, whereas hnRNP A1, by reducing SC35 binding, increases exclusion (34). Thus, the competition provided by an overlapping or a closely abutting pair of enhancer/ silencer represents a simple and frequent mechanism of splicing control.The regulation of Bcl-x alternative splicing has received some attention in recent years leading to the discovery of several cis-acting elements and a few trans-acting control factors (Fig. 1B). Intronic regions downstream from the Bcl-x_L 5′ splice site have been implicated as mediating signals from cytokines such as interleukin-6 and granulocyte-macrophage colony-stimulating factor (35). In addition, we have reported that an element located 187 nt upstream of the Bcl-x_S splice site mediates a protein kinase C-dependent signal that represses splicing to the Bcl-x_S donor site (36). On the other hand, ceramide enhances the use of the Bcl-x_S 5′ splice site by lifting the repression mediated by two other elements (37, 38). The activity of one of these apparently involves SAP155 (39). The RNA-binding protein Sam68, under the control of the tyrosine kinase Fyn, can also increase the production of Bcl-x_S in cooperation with hnRNP A1 (40), and this effect is inhibited by overexpression of ASF/SF2. The Bcl-x sequences bound by the above factors remain to be identified. We also uncovered enhancer elements for Bcl-x_S and Bcl-x_L. hnRNP F and H bind downstream of the Bcl-x_S 5′ splice site to stimulate splicing to that site (41). Enhancement of Bcl-x_L is conferred by SRp30c, which binds upstream of the 5′ splice site to antagonize the repressor activity of pseudo 5′ splice sites (42). Recently, the SR protein SC35 was shown to increase the production of Bcl-x_S (43). Finally, the binding of RBM25 to a sequence element upstream of the Bcl-x_S 5′ splice site stimulated its use, possibly by recruiting U1 snRNP through its interaction with the U1-associated protein hLuc7A (44). Thus, the region located between the two competing 5′ splice sites of Bcl-x is densely populated by splicing control elements.In this study, we have pursued our characterization of Bcl-x splicing control by examining the contribution of sequences directly upstream of the Bcl-x_S donor site. Our mutational approach identified a region containing flanking enhancer and silencer activities. The activity of the repressor portion is mediated by hnRNP K, which makes this protein an anti-apoptotic regulator.     

The Isomerase Active Site of Cyclophilin A Is Critical for Hepatitis C Virus Replication

Cyclosporine A and nonimmunosuppressive cyclophilin (Cyp) inhibitors such as Debio 025, NIM811, and SCY-635 block hepatitis C virus (HCV) replication in vitro. This effect was recently confirmed in HCV-infected patients where Debio 025 treatment dramatically decreased HCV viral load, suggesting that Cyps inhibitors represent a novel class of anti-HCV agents. However, it remains unclear how these compounds control HCV replication. Recent studies suggest that Cyps are important for HCV replication. However, a profound disagreement currently exists as to the respective roles of Cyp members in HCV replication. In this study, we analyzed the respective contribution of Cyp members to HCV replication by specifically knocking down their expression by both transient and stable small RNA interference. Only the CypA knockdown drastically decreased HCV replication. The re-expression of an exogenous CypA escape protein, which contains escape mutations at the small RNA interference recognition site, restored HCV replication, demonstrating the specificity for the CypA requirement. We then mutated residues that reside in the hydrophobic pocket of CypA where proline-containing peptide substrates and cyclosporine A bind and that are vital for the enzymatic or the hydrophobic pocket binding activity of CypA. Remarkably, these CypA mutants fail to restore HCV replication, suggesting for the first time that HCV exploits either the isomerase or the chaperone activity of CypA to replicate in hepatocytes and that CypA is the principal mediator of the Cyp inhibitor anti-HCV activity. Moreover, we demonstrated that the HCV NS5B polymerase associates with CypA via its enzymatic pocket. The study of the roles of Cyps in HCV replication should lead to the identification of new targets for the development of alternate anti-HCV therapies.Hepatitis C virus (HCV)² is the main contributing agent of acute and chronic liver diseases worldwide (1). Primary infection is often asymptomatic or associated with mild symptoms. However, persistently infected individuals develop high risks for chronic liver diseases such as hepatocellular carcinoma and liver cirrhosis (1). The combination of IFNα and ribavirin that serves as current therapy for chronically HCV-infected patients not only has a low success rate (about 50%) (2) but is often associated with serious side effects (2). There is thus an urgent need for the development of novel anti-HCV treatments (2).The immunosuppressive drug cyclosporine A (CsA) was reported to be clinically effective against HCV (3). Controlled trials showed that a combination of CsA with IFNα is more effective than IFNα alone, especially in patients with a high viral load (4, 5). Moreover, recent in vitro studies provided evidence that CsA prevents both HCV RNA replication and HCV protein production in an IFNα-independent manner (6–10). CsA exerts this anti-HCV activity independently of its immunosuppressive activity because the nonimmunosuppressive Cyp inhibitors such as Debio 025, NIM811, and SCY-635 also block HCV RNA and protein production (9, 11–14). Unlike CsA, these molecules do not display calcineurin affinity and specifically inhibit the peptidyl-prolyl cis-trans-isomerase (PPIase) Cyps. Most importantly, recent clinical data demonstrated that Debio 025 dramatically decreased HCV viral load (3.6 log decrease) in patients coinfected with HCV and HIV (15). This 14-day Debio 025 treatment (1200 mg orally administered twice daily) was effective against the three genotypes (genotypes 1, 3, and 4) represented in the study. More recently, the anti HCV effect of Debio 025 in combination with peginterferon α 2a (peg-IFNα2a) was investigated in treatment-inexperienced patients with chronic hepatitis C. Debio 025 (600 mg administered once daily) in combination with peg-IFNα2a (180 μg/week) for 4 weeks induced a continuous decay in viral load that reached −4.61 ± 1.88 IU/ml in patients with genotypes 1 and 4 and −5.91 ± 1.11 IU/ml in patients with genotypes 2 and 3 at week 4 (16). The Debio 025 findings are critical because they suggest that Cyp inhibitors represent a novel class of anti-HCV agents. However, it remains unclear how these compounds control HCV replication. The fact that several recent studies using small RNA interference knockdown approaches suggest that Cyps are critical for the HCV life cycle (9, 17, 18) strongly implies that there is a direct or indirect link between the CsA- and CsA derivative-mediated inhibitory effect on HCV replication and host Cyps.The discovery 20 years ago of the first cellular protein showing PPIase activity (19) was entirely unrelated to the discovery of CypA as an intracellular protein possessing a high affinity for CsA (20). It is only a few years later that Fischer et al. (21) demonstrated that the 18-kDa protein with PPIase activity and CypA represent a single unique protein. All Cyps contain a common domain of 109 amino acids, called the Cyp-like domain, which is surrounded by domains specific to each Cyp members and which dictates their cellular compartmentalization and function (22). Bacteria, fungi, insects, plants, and mammals contain Cyps, which all have PPIase activity and are structurally conserved (22). To date, 16 Cyp members have been identified, and 7 of them are found in humans: CypA, CypB, CypC, CypD, CypE, Cyp40, and CypNK (22).Although there is a growing body of evidence that Cyps control HCV replication in human hepatocytes, a major disagreement currently exists on the respective roles of Cyp members in HCV replication. One study suggests that CypB, but not CypA, is critical for HCV replication (17), another suggests that CypA, but not CypB and CypC, is critical for HCV replication (18), and a third study suggests that three Cyps, CypA, B, and C, are all required for HCV replication (9). Thus, although it becomes evident that Cyps serve as HCV co-factors, their respective contributions and roles in the HCV life cycle remain to be determined. An understanding of the mechanisms that control the Cyp inhibitor-mediated anti-HCV effect is imperative because it will provide new alternate anti-HCV therapies and shed light on the still poorly understood early and late steps of the HCV life cycle.     

Immunity in Chimpanzees Chronically Infected with Hepatitis C Virus: Role of Minor Quasispecies in Reinfection

We have previously reported that chimpanzees chronically infected with hepatitis C virus (HCV) could be reinfected, even with the original infecting strain. In this study we tested the hypothesis that this might reflect the presence of minor quasispecies to which there was little or no immunity. To evaluate this hypothesis, we sequenced multiple clones taken at intervals after primary infection and rechallenge from four chronically infected chimpanzees. The inoculum used in these studies (HCV-H, genotype 1a) revealed 17 separate variants among 46 clones sequenced. Following challenge, each of the four challenged animals showed marked alterations of their quasispecies distribution. The new variants, which appeared 1 to 6 weeks after challenge, were either identical to or closely resembled variants present in the challenge inoculum. These results, paralleled by an increase in viremia in some of the challenged animals, suggest that quasispecies in the challenge inoculum were responsible for signs of reinfection and that there was little immunity. However, the newly emerged quasispecies completely took over infection in only one animal. In the remaining three chimpanzees the prechallenge quasispecies were able to persist. The natural evolution of infection within chimpanzees resulted in variants able to compete with the inoculum variants. Whether through reexposure or the natural progression of infection, newly emerged quasispecies are likely to play a role in the pathogenesis of chronic HCV infection.Hepatitis C virus (HCV) is estimated to chronically infect about 400 million people worldwide. More than half of these develop chronic active hepatitis, cirrhosis, or hepatocellular carcinoma. The HCV genome consists of a single-stranded RNA molecule approximately 10 kb long which contains a single open reading frame encoding approximately 3,000 amino acids (1, 5). There are at least six genotypes of HCV, and within a given patient the genomes are distributed among quasispecies which show sequence variation, particularly in the variable regions of the genome (4, 9). Hypervariable region 1 (HVR1) is a 27-amino-acid segment in the amino terminus of the second envelope protein which has been identified as the most variable region of the viral genome (11, 20). Sequential changes have been observed during the course of chronic HCV infections in chimpanzees and in humans (4, 11, 12). It has been postulated that these reflect immune system selection of neutralizing epitopes encoded by HVR1 (18, 19) and that persistent infection depends on the ability of the virus to continually evade the effects of neutralizing antibody (7, 10, 15, 17, 20). Due to its variability, HVR1 has been used extensively as an indicator of viral evolution.We have previously reported that chronically infected chimpanzees could seemingly be reinfected, even with the original infecting strain (13). In a recent report a similar phenomenon was observed in patients with posttransfusion hepatitis (6). We postulated that this might reflect the presence of minor quasispecies in the inoculum to which there was little or no immunity (13). Here we test this hypothesis by sequencing multiple clones of HVR1 derived at intervals after initial infection and after rechallenge.     

A Role for the M9 Transport Signal of hnRNP A1 in mRNA Nuclear Export

Among the nuclear proteins associated with mRNAs before their export to the cytoplasm are the abundant heterogeneous nuclear (hn) RNPs. Several of these contain the M9 signal that, in the case of hnRNP A1, has been shown to be sufficient to signal both nuclear export and nuclear import in cultured somatic cells. Kinetic competition experiments are used here to demonstrate that M9-directed nuclear import in Xenopus oocytes is a saturable process. Saturating levels of M9 have, however, no effect on the import of either U snRNPs or proteins carrying a classical basic NLS. Previous work demonstrated the existence of nuclear export factors specific for particular classes of RNA. Injection of hnRNP A1 but not of a mutant protein lacking the M9 domain inhibited export of mRNA but not of other classes of RNA. This suggests that hnRNP A1 or other proteins containing an M9 domain play a role in mRNA export from the nucleus. However, the requirement for M9 function in mRNA export is not identical to that in hnRNP A1 protein transport.The transport of macromolecules between the nucleus and cytoplasm is a bi-directional process. The best understood aspect is the import of nuclear proteins that carry a basic nuclear localization signal (NLS)¹ like the simple NLS found in SV-40 T antigen or the bipartite NLS found in nucleoplasmin (Dingwall and Laskey, 1991). Proteins of this class are recognized by the heterodimeric importin receptor, composed of importin α and importin β (for review see Powers and Forbes, 1994; Melchior and Gerace, 1995; Görlich and Mattaj, 1996). The NLS binds directly to the importin α subunit. The importin NLS protein complex docks at the cytoplasmic face of the nuclear pore complex in an energy-independent manner (Newmeyer and Forbes, 1988; Richardson et al., 1988). Subsequently, the small GTPase Ran/TC4 (Melchior et al., 1993; Moore and Blobel, 1993) and a protein of unknown function named variously pp15, p10, or NTF2 (Moore and Blobel, 1994; Paschal and Gerace, 1995) are required for translocation of the NLS-containing complex through the nuclear pore complex.A second major class of imported macromolecules are the uracil rich small nuclear (U sn) RNPs. They do not have a basic NLS but instead have a bipartite nuclear targeting signal. This is composed of an essential signal formed when the Sm core proteins bind to the U snRNA and an additional signal, the trimethyl-guanosine (m₃G) cap, which depending on the cell type or the U snRNA is either essential or required for optimal U snRNP import efficiency (Fischer and Lührmann, 1990; Hamm et al., 1990; Fischer et al., 1993). Kinetic competition experiments have supported the conclusion that U snRNPs require different limiting factors than do NLS-containing proteins for their import and that U snRNPs do not bind to importin α (Fischer et al., 1991, 1993; Michaud and Goldfarb, 1991; van Zee et al., 1993). There is also preliminary evidence that additional different receptors may be required for the nuclear uptake of other RNA species (Michaud and Goldfarb, 1992).Similarly, RNA export from the nucleus relies on recognition of the RNA or RNP export substrates by saturable factors (Zasloff, 1983; Bataillé et al., 1990; Jarmolowski et al., 1994). As for import, evidence for the existence of RNA class-specific export receptors has been obtained from kinetic competition experiments (Jarmolowski et al., 1994). Two RNA-binding proteins have been directly shown to function in RNA export, a nuclear cap binding protein complex in the case of U snRNAs (Izaurralde et al., 1995a ) and the HIV-1 Rev protein in the case of RNAs containing a rev response element (Fischer et al., 1994, 1995). In the case of mRNAs, the best candidates for export mediators are the heterogeneous nuclear (hn) RNP proteins (for review see Piñol-Roma and Dreyfuss, 1993; Izaurralde and Mattaj, 1995).About 20 different hnRNP proteins have been characterized in vertebrate cells (for review see Dreyfuss et al., 1993). The association of hnRNP proteins with mRNA in the nucleus and the cytoplasm suggests that they may regulate and/or facilitate different aspects of gene expression. The possibility that hnRNP proteins might be directly involved in the nucleocytoplasmic trafficking of mRNA molecules was suggested by the observation that several hnRNP proteins, including A1, A2, D, E, I, and K shuttle continuously and rapidly between the nucleus and the cytoplasm and are associated with mRNA in both compartments (Piñol-Roma and Dreyfuss 1992, 1993; Michael et al., 1995a , b). Of these, the best studied example is hnRNP A1. An A1-like hnRNP protein has been shown by immunoelectron microscopy to be associated with a specific mRNA in transit to the cytoplasm through the nuclear pore complex in the insect Chironomus tentans (Visa et al., 1996a ). In mammalian cells, the amount of A1 which is in constant flux between nucleus and cytoplasm is striking. It has been estimated that at least 120,000 molecules of A1 are exported to the cytoplasm per minute but then rapidly reimported such that the steady state localization of A1 is nuclear (Michael et al., 1995a ). Taken together, these results suggest that A1 and other shuttling hnRNP proteins such as A2, D, E, I, and K could play a significant role in the transport of mRNA from the nucleus to the cytoplasm.One key in understanding how hnRNPs may facilitate mRNA export is to determine the signals that mediate their shuttling, i.e., their import into and exit from the nucleus. The nucleocytoplasmic transport of A1 has been recently studied in detail, and the signals that mediate shuttling have been identified (Michael et al., 1995b ; Siomi and Dreyfuss, 1995; Weighardt et al., 1995). Nuclear import of A1 is determined by a 38-amino acid sequence, termed M9, located near the COOH terminus of the protein between amino acids 268 and 305. Its fusion to cytoplasmic reporter proteins such as pyruvate kinase resulted in rapid import of the fusion protein into the nucleus (Siomi and Dreyfuss, 1995). However, the A1 NLS has no sequence similarity to classical protein NLSs such as that of SV-40 large T antigen or nucleoplasmin (Siomi and Dreyfuss, 1995).Surprisingly, M9 also acts as a nuclear export signal (NES). In heterokaryon shuttling assays this domain is necessary and sufficient to allow the export of heterologous proteins, such as the nucleoplasmin core domain (NPLc), which are normally retained in the nucleus (Michael et al., 1995b ). Thus, M9 alone can account for the shuttling of A1. Other hnRNPs such as A2 and B1 bear sequences with striking similarities to M9 (Siomi and Dreyfuss, 1995). Mutagenesis experiments indicate that the NES and NLS activities of M9 are either identical or overlapping as mutants which block M9 NLS activity also abolish NES activity (Michael et al., 1995b ). It is therefore possible that M9 is recognized in the nucleus and the cytoplasm by the same receptor.The second category of NES described was first found in the HIV-1 Rev protein and the inhibitor of protein kinase A (Fischer et al., 1995; Wen et al., 1995; Bogerd et al., 1996; for review see Gerace, 1995). These short, leucine-rich NES sequences bear no relationship to the primary sequence of M9. Furthermore, saturation of the export factor recognized by the Rev NES has no effect on mRNA export (Fischer et al., 1995). A model for mRNA export has been postulated on the basis of the hnRNP data described above. In this model, NES/NLS containing hnRNPs bind in the nucleus to mRNA molecules and deliver them, via the export pathway they access, to the cytoplasm. In the cytoplasm these hnRNP proteins dissociate from the mRNA and return to the nucleus. To further test this model we have analyzed the transport of hnRNP A1 and mRNA in Xenopus laevis oocytes. The oocyte offers a unique opportunity to manipulate specific import or export pathways, like that accessed by M9, and examine the effect on mRNA nuclear export. By using this approach we show here that M9 is, as in somatic cells, a functional NLS in oocytes. Moreover, competition studies indicate that M9 defines a novel class of NLS, since saturation of the M9- mediated import pathway does not interfere with the two previously identified import pathways used by classical NLS-bearing proteins or m₃G-capped-spliceosomal U snRNPs. Injection of an excess of hnRNP A1 but not of a mutant form of the protein lacking the M9 domain, resulted in a specific inhibition of mRNA export, demonstrating that the M9 domain is recognized by a saturable component of the mRNA export machinery. The export of other cellular RNAs such as U snRNAs and tRNA was, in contrast, not affected. Further analysis of mutant hnRNP A1 proteins provides evidence that M9 recognition during mRNA export differs from its recognition during protein transport.     

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

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

VLA-5-mediated Adhesion to Fibronectin Accelerates Hemin-stimulated Erythroid Differentiation of K562 Cells through Induction of VLA-4 Expression

Fibronectin plays important roles in erythropoiesis through the fibronectin receptors VLA-4 and VLA-5. However, the substantial role of these fibronectin receptors and their functional assignment in erythroid differentiation are not yet fully understood. Here, we investigated the effects of cell adhesion to fibronectin on erythroid differentiation using K562 human erythroid progenitor cells. Erythroid differentiation could be induced in K562 cells in suspension by stimulating with hemin. This hemin-stimulated erythroid differentiation was highly accelerated when cells were induced to adhere to fibronectin by treatment with TNIIIA2, a peptide derived from tenascin-C, which has recently been found to induce β1-integrin activation. Another integrin activator, Mn²⁺, also accelerated hemin-stimulated erythroid differentiation. Adhesive interaction with fibronectin via VLA-4 as well as VLA-5 was responsible for acceleration of the hemin-stimulated erythroid differentiation in response to TNIIIA2, although K562 cells should have been lacking in VLA-4. Adhesion to fibronectin forced by TNIIIA2 causally induced VLA-4 expression in K562 cells, and this was blocked by the RGD peptide, an antagonist for VLA-5. The resulting adhesive interaction with fibronectin via VLA-4 strongly enhanced the hemin-stimulated activation of p38 mitogen-activated protein kinase, which was shown to serve as a signaling molecule crucial for erythroid differentiation. Suppression of VLA-4 expression by RNA interference abrogated acceleration of hemin-stimulated erythroid differentiation in response to TNIIIA2. Thus, VLA-4 and VLA-5 may contribute to erythropoiesis at different stages of erythroid differentiation.Hematopoietic stem and progenitor cells proliferate and differentiate in the bone marrow and fetal liver (1–6). Stromal cells of the bone marrow and fetal liver form a hematopoietic microenvironment called a “niche.” This microenvironment niche plays a crucial role in the regulation of the proliferation and differentiation of hematopoietic stem and progenitor cells. Besides humoral factors that include hematopoietic growth factors, adhesive interaction of hematopoietic stem and progenitor cells with stromal cells and/or the extracellular matrix (ECM)² in the hematopoietic microenvironment is indispensable for hematopoietic development (1–6). The ECM in the hematopoietic microenvironment is composed of various macromolecules, such as fibronectin (FN), collagens, laminins, and proteoglycans. Among them, FN is one of the most important parts of the microenvironment niche (7–11). Also, in erythropoiesis, the importance of the adhesion of erythroid progenitors to FN via the FN receptors VLA-4 and VLA-5 has been reported (11–16). However, the substantial role of these FN receptors and their functional assignment in erythroid differentiation are not yet fully understood.We previously found that FN, which provides scaffolding for the adhesion of various cell types, has an alternative functional site opposing cell adhesion (17). A 22-mer peptide derived from the 14th FN type III-like (FNIII) repeat of the FN molecule, termed FNIII14, strongly suppresses cell adhesion to FN by inhibiting the activation of β1-integrins including VLA-4 and VLA-5 (18, 19). Conversely, we have recently found that tenascin (TN)-C, which is an anti-adhesive ECM protein (20, 21), has a functional site for stimulating cell adhesion to FN (22). A 22-mer peptide derived from the FNIII repeat A2 in the TN-C molecule, termed TNIIIA2, can induce the conformational change necessary for functional activation of FN receptors through binding with syndecan-4 (22, 23). The active sites of FNIII14 and TNIIIA2 appear to be cryptic in the molecular structures of FN and TN-C but are exposed by conformational change through interaction with other ECM molecules or by processing with matrix metalloproteinase-2 (22, 24). Thus, these functional sites found in FN and TN-C molecules, which act in opposition to their parental ECM proteins, may act as a negative feedback loop for preventing excessive cellular responses to these ECM proteins in biological processes with ECM rearrangement. In any case, FNIII14 and TNIIIA2 enable us to control, either negatively or positively, the adhesion of various cell types to FN.Various hematopoietic progenitor cell lines have been used in in vitro studies of hematopoietic differentiation. However, most hematopoietic progenitor cell lines are nonadherent, because their cell surface β1-integrins, including FN receptors, have impaired ligand-binding activity (25, 26). Therefore, in order to investigate the role of cell adhesion to FN in hematopoietic differentiation, their FN receptors must be activated. Since TNIIIA2 can induce activation of FN receptors in various hematopoietic progenitor cell lines (22), this peptide factor may be useful for investigating the substantial role of cell adhesion to FN in hematopoietic differentiation. Here, we investigate the effects of cell adhesion to FN on erythroid differentiation using TNIIIA2 and Mn²⁺ as the integrin activator and the human erythroid progenitor cell line K562, which only expresses VLA-5, as the FN receptor (27). As a result, we show that hemin-stimulated erythroid differentiation of K562 cells is strongly enhanced when K562 cells are forced to adhere to FN. Sustained adhesion to FN via VLA-5, which is induced by TNIIIA2 or Mn²⁺, causes induction of VLA-4 expression. The resulting adhesive interaction with FN via newly expressed VLA-4 then generates a conspicuous increase in the hemin-stimulated phosphorylation/activation of p38 MAP kinase, which is shown to serve as a signaling molecule crucial for erythroid differentiation of K562 cells.     

Analysis of PTEN Complex Assembly and Identification of Heterogeneous Nuclear Ribonucleoprotein C as a Component of the PTEN-associated Complex

PTEN (phosphatase and tensin homolog deleted on chromosome 10) is well characterized for its role in antagonizing the phosphoinositide 3-kinase pathway. Previous studies using size-exclusion chromatography demonstrated PTEN recruitment into high molecular mass complexes and hypothesized that PTEN phosphorylation status and PDZ binding domain may be required for such complex formation. In this study, we set out to test the structural requirements for PTEN complex assembly and identify the component(s) of the PTEN complex(es). Our results demonstrated that the PTEN catalytic function and PDZ binding domain are not absolutely required for its complex formation. On the other hand, PTEN phosphorylation status has a significant impact on its complex assembly. Our results further demonstrate enrichment of the PTEN complex in nuclear lysates, suggesting a mechanism through which PTEN phosphorylation may regulate its complex assembly. These results prompted further characterization of other protein components within the PTEN complex(es). Using size-exclusion chromatography and two-dimensional difference gel electrophoresis followed by mass spectrometry analysis, we identified heterogeneous nuclear ribonucleoprotein C (hnRNP C) as a novel protein recruited to higher molecular mass fractions in the presence of PTEN. Further analysis indicates that endogenous hnRNP C and PTEN interact and co-localize within the nucleus, suggesting a potential role for PTEN, alongside hnRNP C, in RNA regulation.Phosphatase and tensin homolog deleted on chromosome 10 (PTEN)⁴ was cloned in 1997 (1–3) and has been well characterized for its tumor-suppressive role by dephosphorylating phosphatidylinositol 3,4,5-trisphosphate to phosphatidylinositol 4,5-bisphosphate and antagonizing the phosphoinositide 3-kinase pathway (4–7). PTEN also regulates cell migration, cell cycle progression, DNA damage response, and chromosome stability independently of its lipid phosphatase activity through its potential protein phosphatase activity and/or protein-protein interaction (8–11) (for recent reviews, see 12–14).PTEN is composed of an N-terminal catalytic domain and a C-terminal regulatory domain. The catalytic domain contains a conserved signature motif (HCXXGXXR) found in dual-specific protein phosphatases, and mutations within this catalytic domain, including the C124S mutation, are known to abrogate PTEN catalytic activity (4). The C terminus of PTEN contains a PDZ (PDS-95/Disc-large/Zo-1) binding domain, which interacts with PDZ-containing proteins such as MAGI-1b, MAGI-2, MAGI-3, hDLG, hMAST and NHERF (15–19). In addition to the PDZ binding domain, several key serine and threonine phosphorylation sites (Ser³⁸⁰, Thr³⁸², Thr³⁸³, and Ser³⁸⁵) at the PTEN C terminus are reported to play an important role in regulating its stability, localization, and activity (20–26).Recent studies suggest that PTEN may function within higher molecular mass complexes. Through size-exclusion chromatography, Vazquez et al. (27) demonstrated that PTEN can be separated into two populations: a monomeric hyperphosphorylated subpopulation and a higher molecular mass hypophosphorylated subpopulation. It was hypothesized that PTEN in its dephosphorylated form can interact with PDZ-containing proteins such as hDLG and be recruited into a higher molecular mass complex. Although the components within PTEN complex(es) have not been systematically studied and purified, MAGI-2, hDLG (27), NHERF2, PDGFR (19), NEP (28), and MVP (29) have been identified as potential components of the PTEN complex using the same size-exclusion chromatography methodology.In this paper, we aim to (i) investigate the essential elements of PTEN required for its complex formation and (ii) dissect the components of the PTEN-associated complex(es). Our results indicate that PTEN catalytic activity or its PDZ binding domain is not absolutely required for complex assembly. PTEN phosphorylation status on amino acids Ser³⁸⁰, Thr³⁸², Thr³⁸³, and Ser³⁸⁵, on the other hand, has a significant role in complex formation. In addition, we demonstrate that the PTEN complex is enriched in nuclear lysates, which suggests a mechanism through which phosphorylation can regulate complex assembly. Using two-dimensional difference gel electrophoresis (DIGE) analysis and comparing proteins present in higher molecular mass fractions in the presence and absence of PTEN followed by mass spectrometry analysis, we have identified heterogeneous nuclear ribonucleoprotein C (hnRNP C) as a potential component within the PTEN complex. PTEN and hnRNP C are shown here to interact and co-localize in the nucleus. We hypothesize that the PTEN and hnRNP C complex may play a role in RNA regulation.     

Algorithms for Finding Small Attractors in Boolean Networks

A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]