LFA-1 and CD2 Synergize for the Erk1/2 Activation in the Natural Killer (NK) Cell Immunological Synapse

Natural killer (NK) cell recognition and formation of a conjugate with target cells, followed by intracellular signal pathway activation and degradation of cytolytic granules, are essential for NK cell cytotoxicity. In this study, NK92 cells were used to investigate synapse formation and subsequent signaling after binding to the target cell. The binding rate of the NK92-target cell was associated with NK92 cell cytotoxicity. Confocal results showed that adhesion molecules, LFA-1 (CD11a) and CD2, accumulated at the interface of the NK92-K562 contact. Ligation with K562 cells activated the Erk1/2 signal pathway of NK92 cells. The blocking of the NK-target conjugate by EDTA or anti-CD11a or/and anti-CD2 antibody decreased the phosphorylation of Erk1/2 and NK cell cytotoxicity. Inhibition of Erk1/2 phosphorylation by the chemical inhibitor U0126 suppressed the cytolytic activity of NK92 cells, but had no effect on NK-target conjugate formation. Thus, conjugate formation of the NK92-target cell was prerequisite to NK cell activation, and subsequent signal transduction was also required for NK cell cytotoxicity.Natural killer (NK)³ cells are a population of granular lymphocytes that play an essential role in cellular immune defense against a variety of tumor cells, virus-infected cells, or allogeneic cells (1–3). NK cells are critical for host immunity for their ability for a quick cytotoxic response and to produce a wide variety of cytokines and chemokines to modulate other cellular components of the immune system (4, 5). NK cells express two functional types of receptors: activating and inhibitory receptors (6–8). The effector function of NK cells is regulated by a balance between opposite signals delivered by the MHC class I-specific inhibitory receptors and the activating receptors responsible for NK cell triggering to permit elimination of pathogens (6).NK cell recognition and binding to target cells, as well as formation of conjugates, are essential for NK cell cytotoxicity (9). Conjugate formation by the NK cell with a target cell is a process mediated by integrins and immunoglobulin superfamily molecules including CD2, CD11a (LFA-1), CD11b, CD11c, and CD28, which also participate in the promotion of NK cell function (10–12). They participate in adhesion between the NK cell and the target cell, and blocking antibodies suppress the adhesion. In addition to possessing an adhesive role, ligation of CD2 induces kinase function and lipid raft polarization (11), whereas ligation of CD11a, CD11b, and CD11c induces phosphorylation-dependent NK cell activation (13, 14). The interaction of specific cell surface receptors with their ligands on a target cell at their interface forms specific activating NK cell immunological synapses and leads to the activation of a cascade of intracellular signals, resulting in Ca²⁺ flux, polarization of granules, and subsequent release of lytic molecules (13, 15, 16). The Erk1/2 (p44/42 mitogen-activated protein kinase) pathway plays an important role in NK cell cytotoxicity (17–21). Inhibition of Erk1/2 might block NK cell cytolytic activity by compromising the release of perforin (22). In this study, the roles of adhesion molecules in NK92-target cell conjugate formation of immunological synapse, and subsequent Erk1/2 activation in NK92 cells was investigated.     

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]     

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]     

Multipattern Consensus Regions in Multiple Aligned Protein Sequences and Their Segmentation

Decomposing a biological sequence into its functional regions is an important prerequisite to understand the molecule. Using the multiple alignments of the sequences, we evaluate a segmentation based on the type of statistical variation pattern from each of the aligned sites. To describe such a more general pattern, we introduce multipattern consensus regions as segmented regions based on conserved as well as interdependent patterns. Thus the proposed consensus region considers patterns that are statistically significant and extends a local neighborhood. To show its relevance in protein sequence analysis, a cancer suppressor gene called p53 is examined. The results show significant associations between the detected regions and tendency of mutations, location on the 3D structure, and cancer hereditable factors that can be inferred from human twin studies.[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]     

Proinsulin and the Genetics of Diabetes Mellitus

Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.     

Angioinhibitory Action of NK4 Involves Impaired Extracellular Assembly of Fibronectin Mediated by Perlecan-NK4 Association

NK4, a fragment of hepatocyte growth factor (HGF), exerts bifunctional action as a competitive antagonist against HGF and its receptor c-Met and an angiogenesis inhibitor. Here we studied the anti-angiogenic mechanism of NK4. In cultured human endothelial cells, NK4 inhibited DNA synthesis induced not only by HGF but also by either basic fibroblast growth factor or vascular endothelial growth factor. Even if c-Met expression was diminished by small interference RNA, NK4 inhibited basic fibroblast growth factor-induced DNA synthesis, indicating that anti-angiogenic action of NK4 is c-Met-independent. Affinity purification with NK4-immobilized beads revealed that NK4 binds to perlecan. Consistent with this, NK4 colocalized with perlecan in endothelial cells. Perlecan is a multidomain heparan sulfate proteoglycan that interacts with basement membrane components such as fibronectin. NK4 inhibited extracellular assembly of fibronectin, by which fibronectin-dependent endothelial cell spreading was inhibited by NK4. Knockdown of perlecan expression by small interference RNA significantly abrogated the inhibitory effect of NK4 on fibronectin assembly and cell spreading. In NK4-treated endothelial cells, tyrosine phosphorylation of focal adhesion kinase and Rac activation were reduced, whereas overexpression of activated Rac recovered the DNA synthesis in NK4-treated endothelial cells. These results indicate that the association between NK4 and perlecan impairs fibronectin assembly, thereby inhibiting anchorage-dependent signaling. The identified mechanism for angiostatic action provides further proof of significance for NK4 in the treatment of cancer and potentially for vascular regulation as well.The manipulation of angiogenesis has potential therapeutic value for the treatment of a variety of diseases including cancer, arthritis, and cardiovascular disease (1, 2). In addition to endothelial cell migration and proliferation, angiogenesis is a process involving dynamic matrix transition (3). During angiogenesis, the vascular basement membrane undergoes proteolytic degradation and transit to the provisional matrix consisting of fibronectin, etc., followed by an intermediate and mature new vascular basement membrane. Growing evidence has shown that such an extracellular matrix (ECM)² not only provides mechanical support to the cells but also essentially regulates cell growth, migration, and survival. The fact that a number of endogenous inhibitors of angiogenesis have been identified from proteolytic fragments of ECM molecules also highlights the important regulatory roles of ECM in angiogenesis (3).NK4 is a proteolytic fragment of hepatocyte growth factor, HGF (4), consisting of an N-terminal hairpin domain and four kringle domains of the α-chain of HGF (5). By competitively binding to HGF receptor c-Met, NK4 acts as an HGF antagonist (5, 6). The NK4 fragment seems to be physiologically generated by mast cells and neutrophils peptidases during inflammation (7). Because HGF regulates malignant behavior in a variety of tumors by inducing invasive, angiogenic, and metastatic responses (8, 9), the blockade of HGF-c-Met signaling by NK4 is a strategy to inhibit tumor invasion and metastasis (6, 9–11). During investigation of a therapeutic approach with NK4 in experimental cancer models, we unexpectedly found that NK4 functions as an angiogenesis inhibitor (12). Based on the bifunctional characteristic as HGF antagonist and angiogenesis inhibitor, NK4 suppressed malignant behavior of cancers, including invasion, metastasis, and angiogenesis-dependent tumor growth (9–12).The angiostatic activity of NK4 is probably independent of its original activity as an HGF antagonist because an anti-HGF antibody capable of preventing HGF-c-Met association did not inhibit human endothelial cell growth stimulated by either bFGF or VEGF (12). However, the mechanism by which NK4 inhibits angiogenic responses in endothelial cells remains to be addressed. In the present study we newly identified perlecan to be an NK4 binding molecule and found that in vascular endothelial cells the association of NK4 with perlecan inhibited extracellular fibronectin assembly, fibronectin-dependent cell spreading, and the subsequent anchorage-dependent signals. Together with our finding that c-Met/HGF receptor is not required for the inhibition of DNA synthesis by NK4, we propose that the association of NK4 with perlecan plays a key role in angiogenesis inhibition by NK4.     

The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the use of wavelet analysis to transform the data obtained under different growth conditions to permit comparison of expression patterns from experiments that have time shifts or delays. We demonstrate this approach using detailed temporal data for a single bacterial gene obtained under 72 different growth conditions. This general strategy can be applied in the analysis of data sets of thousands of genes under different conditions.[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]     

Interdependence of Laminin-mediated Clustering of Lipid Rafts and the Dystrophin Complex in Astrocytes

Astrocyte endfeet surrounding blood vessels are active domains involved in water and potassium ion transport crucial to the maintenance of water and potassium ion homeostasis in brain. A growing body of evidence points to a role for dystroglycan and its interaction with perivascular laminin in the targeting of the dystrophin complex and the water-permeable channel, aquaporin 4 (AQP4), at astrocyte endfeet. However, the mechanisms underlying such compartmentalization remain poorly understood. In the present study we found that AQP4 resided in Triton X-100-insoluble fraction, whereas dystroglycan was recovered in the soluble fraction in astrocytes. Cholesterol depletion resulted in the translocation of a pool of AQP4 to the soluble fraction indicating that its distribution is indeed associated with cholesterol-rich membrane domains. Upon laminin treatment AQP4 and the dystrophin complex, including dystroglycan, reorganized into laminin-associated clusters enriched for the lipid raft markers GM1 and flotillin-1 but not caveolin-1. Reduced diffusion rates of GM1 in the laminin-induced clusters were indicative of the reorganization of raft components in these domains. In addition, both cholesterol depletion and dystroglycan silencing reduced the number and area of laminin-induced clusters of GM1, AQP4, and dystroglycan. These findings demonstrate the interdependence between laminin binding to dystroglycan and GM1-containing lipid raft reorganization and provide novel insight into the dystrophin complex regulation of AQP4 polarization in astrocytes.The basement membrane is a specialized extracellular matrix (ECM)² composed of collagen, fibronectin, perlecan, agrin, and laminin. Several studies have focused on the involvement of these ECM molecules in the formation and maturation of neuromuscular junctions (1–4) and interneuronal synapses (5). More recently, much effort has been made by our group and others to understand the role of these molecules at the interface of astroglia and blood vessels (6–8). Laminin is highly expressed at the perivascular ECM, and the laminin receptor, dystroglycan (α-DG), together with many other components of the dystrophin-associated protein (DAP) complex, is particularly enriched at astrocyte endfeet abutting the blood vessels (9–11). The binding of laminin to α-DG at these specialized astrocyte domains in brain plays a key role in the polarized distribution of components of the DAP complex (6, 12).Multiple lines of evidence indicate that the DAP complex is crucial for the functional distribution both of the water-permeable channel, AQP4, and the inwardly rectifying potassium channel, Kir4.1, at astrocyte endfeet. Indeed, mutations in the dystrophin gene, deletion of α-syntrophin, or loss of laminin binding to α-DG caused by a mutation in the Large1 glycosyltransferase result in a dramatic reduction of the expression of AQP4 and Kir4.1 at perivascular astrocyte endfeet (6, 7, 12–15). The mislocalization of AQP4 in the dystrophin mutant and α-syntrophin null mice results in delayed onset of brain edema and K⁺ clearance (16–18). Collectively, these studies highlight a cooperative role of the ECM and both the extracellular and cytoplasmic components of the DAP complex in the proper targeting of proteins to functional domains of astrocytes leading to the regulation of electrolyte balance and fluid movement.Although the role of DG in targeting other members of the DAP complex (6) as well as AQP4 and Kir4.1 to astrocyte endfeet has been well established (12), the mechanisms underlying this highly organized distribution remain poorly understood. In C2C12 myotubes, agrin triggers AChR clustering, a DG-dependent process, through the coalescence of lipid rafts, which is necessary for proper AChR gating functions (19–21). In oligodendrocytes, laminin induces the relocalization of α6β1 integrin to lipid rafts containing PDGFαR, thereby providing a potential mechanism for the incorporation of cell survival signals (22). Lipid rafts are defined as small (10–200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched domains that compartmentalize cellular processes. These small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions (23). Indeed, the immunological synapse is a good example where rafts are brought together to form large functional membrane domains (24). At the immunological synapse, agrin induces the clustering of lipid rafts and their colocalization with CD3 and CD28 complex surface antigens as well as with Lck tyrosine kinase leading to T cell activation (24). Together, these studies provide evidence for a functional role of ligand-induced clustering of lipid rafts.We have previously shown that laminin induces the coclustering of the DAP complex with Kir4.1 and AQP4 in glial cell cultures (8, 25). Moreover, in vivo studies have shown that the perivascular localization of these channels and several components of the DAP complex at astrocyte endfeet require the interaction of laminin with α-DG (6, 12). In light of these data we asked whether lipid rafts contribute to the laminin-DG-dependent compartmentalization of the DAP complex and AQP4 to key active domains of astrocytes. We show here using fluorescently labeled cholera toxin subunit B (CtxB), a common marker for GM1-containing lipid rafts, that laminin induces a dramatic reorganization of GM1 into large clusters or macrodomains that colocalize extensively with components of the DAP complex in cortical astrocyte cultures. Laminin-mediated clustering of AQP4 is dependent both on cholesterol-sensitive lipid rafts and the DAP complex bringing novel insight into ECM-dependent membrane domain organization and the mechanisms underlying the polarized distribution of these proteins in astrocytes.     

Splitting the BLOSUM Score into Numbers of Biological Significance

Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum). These relate respectively to the sequence convergence (the stochastic similarity of the two protein sequences), to the background frequency divergence (typicality of the amino acid probability distribution in each sequence), and to the target frequency divergence (compliance of the amino acid variations between the two sequences to the protein model implicit in the BLOCKS database). This treatment sharpens the protein sequence comparison, providing a rationale for the biological significance of the obtained score, and helps to identify weakly related sequences. Moreover, the BLOSpectrum can guide the choice of the most appropriate scoring matrix, tailoring it to the evolutionary divergence associated with the two sequences, or indicate if a compositionally adjusted matrix could perform better.[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]     

In Vivo Identification of Nuclear Factors Interacting with the Conserved Elements of Box C/D Small Nucleolar RNAs

The U16 small nucleolar RNA (snoRNA) is encoded by the third intron of the L1 (L4, according to the novel nomenclature) ribosomal protein gene of Xenopus laevis and originates from processing of the pre-mRNA in which it resides. The U16 snoRNA belongs to the box C/D snoRNA family, whose members are known to assemble in ribonucleoprotein particles (snoRNPs) containing the protein fibrillarin. We have utilized U16 snoRNA in order to characterize the factors that interact with the conserved elements common to the other members of the box C/D class. In this study, we have analyzed the in vivo assembly of U16 snoRNP particles in X. laevis oocytes and identified the proteins which interact with the RNA by label transfer after UV cross-linking. This analysis revealed two proteins, of 40- and 68-kDa apparent molecular size, which require intact boxes C and D together with the conserved 5′,3′-terminal stem for binding. Immunoprecipitation experiments showed that the p40 protein corresponds to fibrillarin, indicating that this protein is intimately associated with the RNA. We propose that fibrillarin and p68 represent the RNA-binding factors common to box C/D snoRNPs and that both proteins are essential for the assembly of snoRNP particles and the stabilization of the snoRNA.One of the most interesting recent findings related to ribosome biogenesis has been the identification of a large number of small RNAs localized in the nucleolus (snoRNAs). So far, more than 60 snoRNAs have been identified in vertebrates (17), and more than 30 have been identified in yeast (2). The total number of snoRNAs is not known, but it is likely to be close to 200 (33, 38). These snoRNAs, with the exception of the mitochondrial RNA processing (MRP) species (38), can be grouped into two major families on the basis of conserved structural and sequence elements. The first group includes molecules referred to as box C/D snoRNAs, whereas the second one comprises the species belonging to the box H/ACA family (2, 15).The two families differ in many aspects. The box C/D snoRNAs are functionally heterogeneous. Most of them function as antisense RNAs in site-specific ribose methylation of the pre-rRNA (1, 10, 17, 26); a minority have been shown to play a direct role in pre-rRNA processing in both yeast and metazoan cells (11, 21). The box C/D snoRNAs play their role by means of unusually long (up to 21 contiguous nucleotides) regions of complementarity to highly conserved sequences of 28S and 18S rRNAs (1). In contrast, several members of the H/ACA RNA family have been shown to direct site-specific isomerization of uridines into pseudouridines and to display shorter regions of complementarity to rRNA (14, 24). Mutational analysis suggests that H/ACA snoRNAs can also play a role as antisense RNAs by base pairing with complementary regions on rRNA (15, 24).Another difference between the two families can be seen by comparison of secondary structures. A Y-shaped motif, where a 5′,3′-terminal stem adjoins the C and D conserved elements, has been proposed for many box C/D snoRNAs (16, 26, 40, 42), whereas box H/ACA snoRNAs have been proposed to fold into two conserved hairpin structures connected by a single-stranded hinge region, followed by a short 3′ tail (15).Despite these differences, analogies have been found in the roles played by the conserved box elements. Mutational analysis and competition experiments indicated that C/D and H/ACA boxes are required both for processing and stable accumulation of the mature snoRNA, suggesting that they represent binding sites for specific trans-acting factors (2, 3, 8, 15, 16, 28, 36, 41).All snoRNAs are associated with proteins to form specific ribonucleoparticles (snoRNPs). The study of these particles began only recently, and so far, very few aspects of their structure and biosynthesis have been clarified. The only detailed analysis performed was on the mammalian U3 (19) and the yeast snR30 (20) snoRNPs. Of the identified components, a few appear to be more general factors: fibrillarin, which was shown to be associated with C/D snoRNPs (3, 4, 8, 13, 28, 31, 39), and the nucleolar protein GAR1, which was found associated with H/ACA snoRNAs in yeast (20). Just as the study of small nuclear RNP (snRNP) particles was crucial to the understanding of the splicing process, a detailed structural and functional analysis of snoRNP particles will be essential to elucidate the complex process of ribosome biosynthesis.In this study, we have analyzed the snoRNP assembly of wild-type and mutant U16 snoRNAs by following the kinetics of complex formation in the in vivo system of the Xenopus laevis oocyte. By a UV cross-linking technique, we have identified two proteins, of 40- and 68-kDa apparent molecular mass, which require intact boxes C and D together with the terminal stem for their binding. The 40-kDa species is specifically recognized by fibrillarin antibodies, indicating that this protein is intimately associated with the RNA.     

Proteomics Identification of Drosophila Small Interfering RNA-associated Factors

The Drosophila melanogaster RNA-induced silencing complex (RISC) forms a large ribonucleoprotein particle on small interfering RNAs (siRNAs) and catalyzes target mRNA cleavage during RNA interference (RNAi). Dicer-2, R2D2, Loquacious, and Argonaute-2 are examples of RISC-associated factors that are involved in RNAi. Holo-RISC is an ∼80 S small interfering ribonucleoprotein, which suggests that there are many additional proteins that participate in the RNAi pathway. In this study, we used siRNA affinity capture combined with mass spectrometry to identify novel components of the Drosophila RNAi machinery. Our study identified both established RISC components and novel siRNA-associated factors, many of which contain domains that are consistent with potential roles in RNAi. Functional analysis of these novel siRNA-associated proteins suggests that these factors may play an important role in RNAi.Small RNAs can regulate gene expression through a collection of mechanisms broadly termed RNA silencing. Small RNA-mediated silencing mechanisms occur in most species (1–5). The ability to silence the expression of specific genes using small RNAs via RNA interference (RNAi)¹ has greatly facilitated our understanding of gene function in eukaryotes. In addition, small RNA-mediated gene silencing has therapeutic potential and holds promise for the treatment of specific diseases (6). Understanding the mechanism of RNAi and identifying the components of the RNAi machinery are essential for harnessing its full potential in both genome-wide screens and therapeutic applications.Recently, high throughput sequencing technology has revealed the presence of endogenous siRNAs in plant, fly, worm, and mammalian cells (7–16). These endogenous siRNAs target transposable element RNAs, pseudogene RNAs, and protein-coding mRNAs (17). Therefore, the endogenous siRNA pathway seems to have evolved as a mechanism of cellular defense against selfish genetic elements. The roles of these siRNAs in development and cell physiology are poorly understood.Drosophila melanogaster is a well characterized model system for studying RNAi. In Drosophila, long double-stranded RNAs (dsRNAs) are processed by the endonuclease Dicer-2 into 21-nucleotide siRNAs (18). After processing, these siRNAs form an initiator complex with Dicer-2 and the dsRNA-binding domain (dsRBD)-containing protein R2D2 (19–23). This R2D2-Dicer-2 Initiator (RDI) complex transitions to a larger siRNP called the RISC loading complex (21, 22, 24, 25) and then to pre-RISC (26). Subsequently, pre-RISC matures into holo-RISC, which includes the catalytic activity necessary for target mRNA cleavage (21, 25, 27). The endonuclease subunit responsible for target cleavage in holo-RISC is Argonaute-2 (Ago2) (28, 29), which uses the guide strand of the siRNA duplex to target complementary mRNA sequences for cleavage and degradation.Studies of the RDI complex strongly suggest that it includes no other proteins besides Dicer-2 and R2D2 (22). Additional proteins such as Ago2 are present in pre-RISC and holo-RISC, but nonetheless the complete compositions of the RISC loading complex, pre-RISC, and holo-RISC are unknown. Furthermore, holo-RISC sediments at ∼80 S during sucrose gradient centrifugation (30). These observations indicate that additional protein factors associate with siRNAs. In this study, we identified siRNA-binding proteins from Drosophila embryo extracts. Target cleavage assays and immunoblotting of our siRNA affinity-selected proteins suggest that we purified active holo-RISC components. Proteomics analysis of the affinity matrix revealed both established and novel siRNA-associated proteins. Functional analyses of a subset of these factors suggest that they play important roles in RNAi.     

Sip1, a Novel RS Domain-Containing Protein Essential for Pre-mRNA Splicing

Previous studies have shown that protein-protein interactions among splicing factors may play an important role in pre-mRNA splicing. We report here identification and functional characterization of a new splicing factor, Sip1 (SC35-interacting protein 1). Sip1 was initially identified by virtue of its interaction with SC35, a splicing factor of the SR family. Sip1 interacts with not only several SR proteins but also with U1-70K and U2AF65, proteins associated with 5′ and 3′ splice sites, respectively. The predicted Sip1 sequence contains an arginine-serine-rich (RS) domain but does not have any known RNA-binding motifs, indicating that it is not a member of the SR family. Sip1 also contains a region with weak sequence similarity to the Drosophila splicing regulator suppressor of white apricot (SWAP). An essential role for Sip1 in pre-mRNA splicing was suggested by the observation that anti-Sip1 antibodies depleted splicing activity from HeLa nuclear extract. Purified recombinant Sip1 protein, but not other RS domain-containing proteins such as SC35, ASF/SF2, and U2AF65, restored the splicing activity of the Sip1-immunodepleted extract. Addition of U2AF65 protein further enhanced the splicing reconstitution by the Sip1 protein. Deficiency in the formation of both A and B splicing complexes in the Sip1-depleted nuclear extract indicates an important role of Sip1 in spliceosome assembly. Together, these results demonstrate that Sip1 is a novel RS domain-containing protein required for pre-mRNA splicing and that the functional role of Sip1 in splicing is distinct from those of known RS domain-containing splicing factors.Pre-mRNA splicing takes place in spliceosomes, the large RNA-protein complexes containing pre-mRNA, U1, U2, U4/6, and U5 small nuclear ribonucleoprotein particles (snRNPs), and a large number of accessory protein factors (for reviews, see references 21, 22, 37, 44, and 48). It is increasingly clear that the protein factors are important for pre-mRNA splicing and that studies of these factors are essential for further understanding of molecular mechanisms of pre-mRNA splicing.Most mammalian splicing factors have been identified by biochemical fractionation and purification (3, 15, 19, 31–36, 45, 69–71, 73), by using antibodies recognizing splicing factors (8, 9, 16, 17, 61, 66, 67, 74), and by sequence homology (25, 52, 74).Splicing factors containing arginine-serine-rich (RS) domains have emerged as important players in pre-mRNA splicing. These include members of the SR family, both subunits of U2 auxiliary factor (U2AF), and the U1 snRNP protein U1-70K (for reviews, see references 18, 41, and 59). Drosophila alternative splicing regulators transformer (Tra), transformer 2 (Tra2), and suppressor of white apricot (SWAP) also contain RS domains (20, 40, 42). RS domains in these proteins play important roles in pre-mRNA splicing (7, 71, 75), in nuclear localization of these splicing proteins (23, 40), and in protein-RNA interactions (56, 60, 64). Previous studies by us and others have demonstrated that one mechanism whereby SR proteins function in splicing is to mediate specific protein-protein interactions among spliceosomal components and between general splicing factors and alternative splicing regulators (1, 1a, 6, 10, 27, 63, 74, 77). Such protein-protein interactions may play critical roles in splice site recognition and association (for reviews, see references 4, 18, 37, 41, 47 and 59). Specific interactions among the splicing factors also suggest that it is possible to identify new splicing factors by their interactions with known splicing factors.Here we report identification of a new splicing factor, Sip1, by its interaction with the essential splicing factor SC35. The predicted Sip1 protein sequence contains an RS domain and a region with sequence similarity to the Drosophila splicing regulator, SWAP. We have expressed and purified recombinant Sip1 protein and raised polyclonal antibodies against the recombinant Sip1 protein. The anti-Sip1 antibodies specifically recognize a protein migrating at a molecular mass of approximately 210 kDa in HeLa nuclear extract. The anti-Sip1 antibodies sufficiently deplete Sip1 protein from the nuclear extract, and the Sip1-depleted extract is inactive in pre-mRNA splicing. Addition of recombinant Sip1 protein can partially restore splicing activity to the Sip1-depleted nuclear extract, indicating an essential role of Sip1 in pre-mRNA splicing. Other RS domain-containing proteins, including SC35, ASF/SF2, and U2AF65, cannot substitute for Sip1 in reconstituting splicing activity of the Sip1-depleted nuclear extract. However, addition of U2AF65 further increases splicing activity of Sip1-reconstituted nuclear extract, suggesting that there may be a functional interaction between Sip1 and U2AF65 in nuclear extract.