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Results for “Subcellular localization”

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At least 667 records · Page 37Linked to original sources

PubMed1999

Differential subcellular localization of DNA-dependent protein kinase components Ku and DNA-PKcs during mitosis.

The Ku protein is a complex of two subunits, Ku70 and Ku80. Ku plays an important role in DNA-PKcs-dependent double-strand break repair and V(D)J recombination, and in growth regulation, which is DNA-PKcs-independent. We studied the expression and the subcellular localization of Ku and DNA-PKcs throughout the cell cycle in several established human cell lines. Using immunofluorescence analysis and confocal laser scanning microscopy, we detected Ku70 and Ku80 in the nuclei in interphase cells. In mitotic cells (1) most of Ku protein was found diffused in the cytoplasm, (2) a fraction was detected at the periphery of condensed chromosomes, (3) no Ku protein was present in the chromosome interior. Association of Ku with isolated chromosomes was also observed. On the other hand, DNA-PKcs was detected in the nucleus in interphase cells and not at the periphery of condensed chromosomes during mitosis. Using indirect immunoprecipitation, we found that throughout the cell cycle, Ku70 and Ku80 were present as heterodimers, some in complex with DNA-PKcs. Our findings suggest that the localization of Ku at the periphery of metaphase chromosomes might be imperative for a novel function of Ku in the G(2)/M phase, which does not require DNA-PKcs.

Antigens, Nuclear↗

PubMed1995

Characterization, subcellular localization, and developmental regulation of a cysteine proteinase from Dictyostelium discoideum.

Previous studies showed that vegetative cells of Dictyostelium discoideum make a cysteine proteinase called proteinase-1, which contains multiple residues of GlcNAc-1-P linked directly to peptidyl serines. As a prelude to understanding the function of this novel carbohydrate modification, we purified and extensively characterized this proteinase in terms of its enzymatic activity, subcellular localization, and developmental regulation. The purified enzyme has an apparent molecular weight of 38 kDa in heat-denatured, reducing SDS/PAGE and 55 kDa under nonreducing conditions. Native gel electrophoresis and isoelectric focusing revealed two protein bands with equal activity and having pI values of 2.5 and 2.6. Even more complex patterns are found in non-heat-denatured SDS/PAGE gels. However, partial amino acid sequencing of the purified protein gave predominantly a single sequence. The enzyme is inhibited by trans-epoxysuccinyl-L-leucylamido-(4-guanidino) butane, Na-p-tosyl-L-lysine chloromethyl ketone, N-tosyl-L-phenylalanine chloromethyl ketone, and leupeptin, has a pH optimum of 5.0, and cofractionates with lysosomal enzymes in bacterially grown cells. It appears to comprise about 90% of the total cysteine proteinase activity in cells at a time when the cells have just finished clearing the bacterial lawn. Prior to this point and after the onset of development, its level is 2- to 20-fold lower. This remarkably fine regulation parallels the developmental regulation of other cysteine proteinases in Dictyostelium. Based on these results it appears that proteinase-1 may be primarily used for specialized proteolysis just before the onset of development rather than for simply digesting the bacteria for food.

Amino Acid Sequence↗

PubMed2004

Predicting subcellular localization of proteins using machine-learned classifiers.

MOTIVATION: Identifying the destination or localization of proteins is key to understanding their function and facilitating their purification. A number of existing computational prediction methods are based on sequence analysis. However, these methods are limited in scope, accuracy and most particularly breadth of coverage. Rather than using sequence information alone, we have explored the use of database text annotations from homologs and machine learning to substantially improve the prediction of subcellular location. RESULTS: We have constructed five machine-learning classifiers for predicting subcellular localization of proteins from animals, plants, fungi, Gram-negative bacteria and Gram-positive bacteria, which are 81% accurate for fungi and 92-94% accurate for the other four categories. These are the most accurate subcellular predictors across the widest set of organisms ever published. Our predictors are part of the Proteome Analyst web-service.

Algorithms↗

PubMed1998

Purification of guinea pig small intestinal peroxisomes and the subcellular localization of glucose-6-phosphate dehydrogenase.

A method for the isolation of highly purified peroxisomes from guinea pig small intestine was developed. This two-stage process involved a rate-dependent banding of a light-mitochondria lambda-fraction followed by a density-dependent banding of the catalase enriched fractions obtained from the first step, using a horizontal rotor. Furthermore, the subcellular localization of glucose-6-phosphate dehydrogenase (NADP+-dependent) activity in guinea pig small intestine was examined. Analysis of density-gradient fractions indicated that approximately 3-4% of the cellular NADP+-dependent glucose-6-phosphate dehydrogenase activity is associated with peroxisomal fractions and that it is localized to the matrix of peroxisomes. It is therefore suggested that a peroxisomal source of NADPH may be utilized by enzyme systems that use NADPH specifically as a reductant.

Animals↗

PubMed2001

Molecular dissection of actopaxin-integrin-linked kinase-Paxillin interactions and their role in subcellular localization.

Paxillin is a focal adhesion adapter protein involved in integrin signaling. We have recently reported that the paxillin LD1 motif acts as a binding interface for both the actin-binding protein actopaxin and the serine/threonine integrin-linked kinase (ILK). In this report we demonstrate the direct association between actopaxin and ILK and dissect the role of the respective interactions in their subcellular localization. Co-immunoprecipitation experiments were employed to map the binding sites on ILK and actopaxin. ILK binds to the CH2 domain of actopaxin. However, an actopaxin CH2 domain mutant defective for paxillin binding (paxillin binding subdomain mutant) retains the capacity to bind ILK, indicating that paxillin and ILK binding sites on actopaxin are distinct. Actopaxin binds to the C terminus of ILK. Despite the direct binding between actopaxin and ILK, mutation analysis confirmed a primary role for paxillin in their localization to focal adhesions. Interestingly, an ILK mutant (E359K) that was previously reported to act as dominant negative for ILK function was unable to bind actopaxin or paxillin and failed to localize to focal adhesions. This mutant also exhibited in vitro kinase activity comparable with wild-type ILK. Taken together, these data suggest that normal ILK signaling is dependent on efficient localization involving multiple protein interactions.

Actinin↗

PubMed2001

Expression, activity, and subcellular localization of the Yin Yang 1 transcription factor in Xenopus oocytes and embryos.

Yin Yang 1 (YY1) is a multifunctional transcription factor that acts as an activator, repressor, or initiator of transcription of numerous cellular and viral genes. Previous studies in tissue culture model systems suggest YY1 plays a role in development and differentiation in multiple cell types, but the biological role of YY1 in vertebrate oocytes and embryos is not well understood. Here we analyzed expression, activity, and subcellular localization profiles of YY1 during Xenopus laevis development. Abundant levels of YY1 mRNA and protein were detected in early stage oocytes and in all subsequent stages of oocyte and embryonic development through to swimming larval stages. The DNA binding activity of YY1 was detected only in early oocytes (stages I and II) and in embryos after the midblastula transition (MBT), which suggested that its potential to modulate gene expression may be specifically repressed in the intervening period of development. Experiments to determine transcriptional activity showed that addition of YY1 recognition sites upstream of the thymidine kinase promoter had no stimulatory or repressive effect on basal transcription in oocytes and post-MBT embryos. Although the apparent transcriptional inactivity of YY1 in oocytes could be explained by the absence of DNA binding activity at this stage of development, the lack of transcriptional activity in post-MBT embryos was not expected given the ability of YY1 to bind its recognition elements. Subsequent Western blot and immunocytochemical analyses showed that YY1 is localized in the cytoplasm in oocytes and in cells of developing embryos well past the MBT. These findings suggest a novel mode of YY1 regulation during early development in which the potential transcriptional function of the maternally expressed factor is repressed by cytoplasmic localization.

Animals↗

PubMed2004

Requirements of cyclin a for mitosis are independent of its subcellular localization.

Cyclin A (CycA), the only essential mitotic cyclin in Drosophila, is cytoplasmic during interphase and accumulates in the nucleus during prophase. We show that interphase localization is mediated by Leptomycin B (LMB)-sensitive nuclear export. This is a feature shared with human CyclinB1, and it is assumed that nuclear accumulation is necessary for mitotic entry. Here, we tested if the unique mitotic function of CycA requires nuclear accumulation. We fused subcellular localization signals to CycA and tested their mitotic capability. Surprisingly, nuclear accumulation was not required, and even a membrane-tethered form of CycA was able to induce mitosis. We noted that Cyclin B (CycB) protein disappears prematurely in CycA mutants, reminiscent of rca1 mutants. Rca1 is an inhibitor of Fizzy-related-APC/C activity, and in rca1 mutants, mitotic cyclins are degraded in G2 of the 16(th) embryonic cell cycle. Overexpression of Rca1 can restore mitosis in CycA mutants, indicating that the mitotic failure of CycA mutants is caused by premature activation of the APC/C. The essential mitotic function of CycA is therefore not the activation of numerous mitotic substrates by Cdk1-dependent phosphorylation. Rather, CycA-dependent kinase activity is required to inhibit one inhibitor of mitosis, the Fzr protein.

Animals↗

PubMed1997

Cloning and subcellular localization of hamster and rat isopentenyl diphosphate dimethylallyl diphosphate isomerase. A PTS1 motif targets the enzyme to peroxisomes.

To date, isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IPP isomerase; EC 5.3.3.2) is presumed to have a cytosolic localization. However, we have recently shown that in permeabilized cells lacking cytosolic components, mevalonate can be converted to cholesterol, implying that all of the enzymes required for the conversion of mevalonate to farnesyl diphosphate are found in the peroxisome. To provide unequivocal evidence for the subcellular localization of IPP isomerase, in this study, we have cloned the rat and hamster homologues of IPP isomerase and identified the signal that targets this enzyme to peroxisomes. In addition, we also demonstrate that IPP isomerase is regulated at the mRNA level.

Amino Acid Sequence↗

PubMed2004

A CRM1-dependent nuclear export pathway is involved in the regulation of IRF-5 subcellular localization.

Interferon regulatory factors (IRFs) are involved in gene regulation in many biological processes including the antiviral, growth regulatory, and immune modulatory functions of the interferon system. Several studies have demonstrated that IRF-3, IRF-5, and IRF-7 specifically contribute to the innate antiviral response to virus infection. It has been reported that virus-specific phosphorylation leads to IRF-5 nuclear localization and up-regulation of interferon, cytokine, and chemokine gene expression. Two nuclear localization signals have been identified in IRF-5, both of which are sufficient for nuclear translocation and retention in virus-infected cells. In the present study, we demonstrate that a CRM1-dependent nuclear export pathway is involved in the regulation of IRF-5 subcellular localization. IRF-5 possesses a functional nuclear export signal (NES) that controls dynamic shuttling between the cytoplasm and the nucleus. The NES element is dominant in unstimulated cells and results in the predominant cytoplasmic localization of IRF-5. Mutation of two leucine residues in the NES motif to alanine, or three adjacent Ser/Thr residues to the phosphomimetic Asp, results in constitutively nuclear IRF-5 and suggests that phosphorylation of adjacent Ser/Thr residues may contribute to IRF-5 nuclear accumulation in virus-induced cells. IKK-related kinases TBK1 and IKKepsilon have been shown to phosphorylate and activate IRF-3 and IRF-7, leading to the production of type 1 interferons and the development of a cellular antiviral state. We examined the phosphorylation and activation of IRF-5 by TBK1 and IKKepsilon kinases. Although IRF-5 is phosphorylated by IKKepsilon and TBK1 in co-transfected cells, the phosphorylation of IRF-5 did not lead to IRF-5 nuclear localization or activation.

Active Transport, Cell Nucleus↗

PubMed2006

A novel method for apoptosis protein subcellular localization prediction combining encoding based on grouped weight and support vector machine.

Apoptosis proteins have a central role in the development and homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. Based on the idea of coarse-grained description and grouping in physics, a new feature extraction method with grouped weight for protein sequence is presented, and applied to apoptosis protein subcellular localization prediction associated with support vector machine. For the same training dataset and the same predictive algorithm, the overall prediction accuracy of our method in Jackknife test is 13.2% and 15.3% higher than the accuracy based on the amino acid composition and instability index. Especially for the else class apoptosis proteins, the increment of prediction accuracy is 41.7 and 33.3 percentile, respectively. The experiment results show that the new feature extraction method is efficient to extract the structure information implicated in protein sequence and the method has reached a satisfied performance despite its simplicity. The overall prediction accuracy of EBGW_SVM model on dataset ZD98 reach 92.9% in Jackknife test, which is 8.2-20.4 percentile higher than other existing models. For a new dataset ZW225, the overall prediction accuracy of EBGW_SVM achieves 83.1%. Those implied that EBGW_SVM model is a simple but efficient prediction model for apoptosis protein subcellular location prediction.

Algorithms↗

PubMed2001

hMYH cell cycle-dependent expression, subcellular localization and association with replication foci: evidence suggesting replication-coupled repair of adenine:8-oxoguanine mispairs.

The human MutY homolog, hMYH, is an adenine-specific DNA glycosylase that removes adenines or 2-hydroxyadenines mispaired with guanines or 8-oxoguanines. In order to prevent mutations, this activity must be directed to the newly synthesized strand and not the template strand during DNA synthesis. The subcellular localization and expression of hMYH has been studied in serum-stimulated, proliferating MRC5 cells. Using specific antibodies, we demonstrate that endogenous hMYH protein localized both to nuclei and mitochondria. hMYH in the nuclei is distinctly distributed and co-localized with BrdU at replication foci and with proliferating cell nuclear antigen (PCNA). The levels of hMYH in the nucleus increased 3- to 4-fold during progression of the cell cycle and reached maximum levels in S phase compared to early G(1). Similar results were obtained for PCNA, while there were no notable changes in expression of 8-oxoguanine glycosylase or the human MutT homolog, MTH1, throughout the cell cycle. The cell cycle-dependent expression and localization of hMYH at sites of DNA replication suggest a role for this glycosylase in immediate post-replication DNA base excision repair.

Adenine↗

PubMed2005

Expression and subcellular localization of WAVE isoforms in the megakaryocyte/platelet lineage.

WAVE isoforms, which consist of WAVE-1, WAVE-2 and WAVE-3, are members of the Wiskott-Aldrich syndrome protein (WASP) family. They are implicated in the regulation of actin-cytoskeletal reorganization downsteam of the small GTPase, Rac. Since platelet attachment to extracellular matrices leads to filopodial and lamellipodial extension, we examined the expression and subcellular localization of WAVEs in platelets. Employing primary megakaryocytic cells derived from cord blood as well as megakaryocytic cell lines, we also examined their expression during megakaryocytic differentiation. Immunoblotting and immunohistochemical analysis revealed that platelets expressed WAVE-1 and WAVE-2, whereas WAVE-3 expression was hardly to be detected. WAVE-1 expression was associated with megakaryocytic differentiation, whereas WAVE-2 and WAVE-3 expression was not changed by the differentiation. In adhered platelets both WAVE-1 and WAVE-2 were localized at the edge of the lamellipodia and at the tips of filopodia. In WASP-deficient platelets we found normal lamellipodial formation and localization of WAVE-1 and WAVE-2 at the edges of lamellipodia. Furthermore, we demonstrated that WAVE-1 and WAVE-2 moved from a detergent-soluble cytosolic fraction to insoluble cytoskeleton fraction after platelet aggregation. These results suggest that WAVE-1 and WAVE-2 regulate actin reorganization during platelet spreading and aggregate formation.

Blood Platelets↗

PubMed2000

Subcellular localization and processing of the lytic transglycosylase of the conjugative plasmid R1.

Protein P19 encoded by the conjugative resistance plasmid R1, is essential for efficient conjugative DNA transfer and infection by the pilus-specific RNA phage R17. Based on sequence homologies P19 belongs to a family of lysozyme-like virulence factors which are found in type III and type IV secretion systems. In this report we describe the processing and subcellular localization of P19. Pulse-chase experiments were used to demonstrate the processing of P19 by the signal peptidase I of Escherichia coli. Translocation of P19 across the inner membrane was shown by gene 19-phoA fusions. Cell fractionation studies of P19 expressing cells showed the presence of P19 in the membrane compartment. P19 was solubilized with the detergent Sarkosyl indicating an inner membrane localization. Using sucrose density gradient centrifugation to separate inner and outer membranes, P19 was found in both membrane fractions. Taken together, our data suggest that mature P19 is a periplasmic protein which may be attached to the proposed membrane-spanning DNA transport complex.

Alkaline Phosphatase↗

PubMed1996

Protein kinase C isoforms epsilon, eta, delta and zeta in murine adipocytes: expression, subcellular localization and tissue-specific regulation in insulin-resistant states.

The Ca(2+)-insensitive protein kinase C (PKC) isoforms epsilon, eta, delta and zeta are possible direct downstream targets of phosphatidylinositol 3-kinase (P13-K), and might therefore be involved in insulin signalling. Although isoform-specific changes in PKC expression have been reported for skeletal muscle and liver in insulin-resistant states, little is known about these isoforms in adipocytes. Therefore we studied (1) expression and subcellular localization of these isoforms in murine adipocytes, (2) translocation of specific isoforms to membranes in response to treatment with insulin and phorbol 12-myristate 13-acetate (PMA) and (3) regulation of expression in insulin-resistant states. The PKC isoforms epsilon, eta, delta and zeta are expressed in adipocytes. Immunoreactivity for all isoforms is higher in the membranes than in the cytosol, but subcellular fractionation by differential centrifugation shows an isoform-specific distribution within the membrane fractions. PMA treatment of adipocytes induces translocation of PKC-epsilon and -delta from the cytosol to the membrane fractions. Insulin treatment does not alter the subcellular distribution of any of the isoforms. 3T3-L1 adipocytes express PKC-epsilon and -zeta, and PKC-epsilon expression increases with differentiation from preadipocytes to adipocytes. PKC-epsilon expression decreases in an adipose-specific and age/obesity-dependent manner in two insulin-resistant models, the brown-adipose-tissue-deficient mouse and db/db mouse compared with control mice. We conclude that, although none of the isoforms investigated seems to be activated by insulin, the decrease in PKC-epsilon expression might contribute to metabolic alterations in adipocytes associated with insulin resistance and obesity.

3T3 Cells↗

PubMed1990

Chain elongation of fatty acids in rat small intestine: subcellular localization and effects of clofibrate and partially hydrogenated fish oil.

Clofibrate treatment was found to increase by a factor of two the activity of malonyl-CoA-dependent palmitic acid chain elongation in crude 'microsomal' fractions isolated from rat small intestine. A slight stimulation was indicated also after feeding a high fat diet containing partially hydrogenated fish oil (PHFO). This effect was, however, not statistically significant. Subcellular localization of this chain elongation activity was studied by Nycodenz gradient centrifugation. Chain elongation of palmitic acid was observed only in fractions containing high esterase activity, suggesting a microsomal localization. Similar distributions were seen after feeding the peroxisomal proliferators clofibrate and PHFO. Chain-shortening activity was found in the fractions containing high catalase activity, confirming our earlier studies suggesting a peroxisomal localization of this activity also in rat small intestine.

Acetyltransferases↗

PubMed1996

Cellular and subcellular localization of acetaldehyde-protein adducts in liver biopsies from alcoholic patients.

Acetaldehyde, the first product of ethanol in hepatocytes, can react with protein to form acetaldehyde-protein adducts (APAs). Because it has been suggested that these adducts could be involved in the pathogenesis of ethanol-induced hepatic lesions and in fibrogenesis, we performed an ultrastructural immunohistochemical study to precisely define the cellular and subcellular localization of APAs. A preembedding technique of indirect immunoperoxidase was performed in liver biopsy specimens from eight patients with alcoholic liver disease, using a specific antiserum against APAs. In all specimens, APAs were detected in the rough endoplasmic reticulum, in some peroxisomes, and in the cytosol of hepatocytes. In four patients with steatofibrosis or cirrhosis, labeling of Ito cells was also observed. In these cases, the same staining pattern was observed in the cytoplasmic processes of myofibroblasts in areas of fibrogenesis. When isolated rat Ito cells were incubated in the presence of acetaldehyde, APAs were also detected in the cytoplasm. These results show that APA formation occurs in hepatocytes at the sites of acetaldehyde production. Detection of APAs in human and rat Ito cells strongly suggests that acetaldehyde can diffuse into Ito cells and bind to cytoplasmic proteins to form local APAs. Because Ito cells are the main effector cells of liver fibrosis, detection of APAs in these cells points to their possible involvement in liver fibrogenesis.

Acetaldehyde↗

PubMed2005

Subcellular localization of glucose transporter 4 in the hypothalamic arcuate nucleus of ob/ob mice under basal conditions.

Glucose transporter (GLUT) 4 plays an important role in insulin-induced glucose uptake in skeletal muscle and white adipose tissue. Although GLUT4 is abundant in the hypothalamus as well as in these peripheral tissues, little is known about the role of GLUT4 in the hypothalamus. In this study, we examined the subcellular localization of GLUT4 and the activation of insulin signaling pathways in the hypothalamic arcuate nucleus of ob/ob mice under basal conditions. The expression of GLUT4 in the arcuate nucleus of ob/ob mice was higher than that in lean mice. Interestingly, GLUT4 on the plasma membrane increased significantly in neurons of the arcuate nucleus of ob/ob mice when compared to that in lean mice. Because serum insulin levels of ob/ob mice were very high, we hypothesized that insulin strongly stimulates GLUT4 translocation in the arcuate nucleus of ob/ob mice. Unexpectedly, tyrosine phosphorylation of IR and insulin receptor substrate-1 (IRS-1) was faint in the hypothalamus of lean and ob/ob mice. In addition, phosphorylation of IRS-1 at Ser307 in the hypothalamus of ob/ob mice was higher when compared to that in lean mice, suggesting that insulin signaling is impaired by phosphorylation of IRS-1 at Ser307 in the hypothalamus of ob/ob mice. However, serine phosphorylation of Akt in the arcuate nucleus of ob/ob mice increased significantly when compared to that in lean mice. Furthermore, the expression of brain-derived neurotrophic factor, an activator of PI3K-Akt pathway in neurons, increased significantly in the ventromedial hypothalamus of ob/ob mice. We discuss the possibility of novel pathways which induce the translocation of GLUT4 in the arcuate nucleus of ob/ob mice.

Animals↗

PubMed1995

Changes in the subcellular localization of replication initiation proteins and cell cycle proteins during G1- to S-phase transition in mammalian cells.

DNA replication in eukaryotic cells is restricted to the S-phase of the cell cycle. In a cell-free replication model system, using SV40 origin-containing DNA, extracts from G1 cells are inefficient in supporting DNA replication. We have undertaken a detailed analysis of the subcellular localization of replication proteins and cell cycle regulators to determine when these proteins are present in the nucleus and therefore available for DNA replication. Cyclin A and cdk2 have been implicated in regulating DNA replication, and may be responsible for activating components of the DNA replication initiation complex on entry into S-phase. G1 cell extracts used for in vitro replication contain the replication proteins RPA (the eukaryotic single-stranded DNA binding protein) and DNA polymerase alpha as well as cdk2, but lack cyclin A. On localizing these components in G1 cells we find that both RPA and DNA polymerase alpha are present as nuclear proteins, while cdk2 is primarily cytoplasmic and there is no detectable cyclin A. An apparent change in the distribution of these proteins occurs as the cell enters S-phase. Cyclin A becomes abundant and both cyclin A and cdk2 become localized to the nucleus in S-phase. In contrast, the RPA-34 and RPA-70 subunits of RPA, which are already nuclear, undergo a transition from the uniform nuclear distribution observed during G1, and now display a distinct punctate nuclear pattern. The initiation of DNA replication therefore most likely occurs by modification and activation of these replication initiation proteins rather than by their recruitment to the nuclear compartment.

Base Sequence↗