Matrin CYP, an SR-rich cyclophilin that associates with the nuclear matrix and splicing factors

We report the identification and cloning of a nuclear matrix protein termed matrin cyclophilin or matrin CYP. The derived sequence of matrin cyp encodes a protein of 752 amino acids with a predicted mass of 88 kDa. A 172-residue stretch at the amino terminus shows high identity with the ubiquitous family of cyclophilins. Clustered throughout the carboxyl half of the protein are a series of serine-arginine (SR) repeats that are a characteristic feature of many RNA splicing factors. Antibodies raised against matrin CYP recognize a 106-kDa antigen that is detected in isolated nuclei and quantitatively subfractionates in the nuclear matrix. Laser scanning confocal microscopy localizes most of the anti-matrin CYP-specific antigen within the nucleus in a pattern of large bright speckles that co-localize with splicing factors and diffuse nucleoplasmic staining. A strikingly similar pattern of staining is observed in cells extracted for in situ nuclear matrices. A fusion protein containing the cyclophilin domain of matrin CYP exhibits cyclosporin A (CsA)-sensitive, peptidylprolyl cis-trans-isomerase activity that is characteristic of native cyclophilins. Although total rat liver nuclei contains predominantly CsA-resistant PPIase activity, the corresponding activity in the nuclear matrix is largely CsA-sensitive.     

Cloning of AIP1, a novel protein that associates with the apoptosis-linked gene ALG-2 in a Ca2+-dependent reaction

ALG-2 is a 22-kDa calcium-binding protein necessary for cell death induced by different stimuli in 3DO T-cell hybridoma. 3DO cell clones depleted of ALG-2 protein exhibit normal caspases activation, suggesting that ALG-2 function is required downstream or is independent of caspase proteases activity for apoptosis to occur. Using the yeast two-hybrid screening system, we have isolated and characterized the mouse cDNA encoding for ALG-2 interacting protein 1 (AIP1), a novel protein that interacts with ALG-2. ALG-2 and AIP1 colocalize in the cytosol and the presence of calcium is an indispensable requisite for their association. Sequence alignment shows that AIP1 is highly similar to BRO1, a yeast protein related to components of the Pkc1p-MAP kinase cascade. Overexpression of a truncated form of AIP1 protects two different cell types from death induced by trophic factors withdrawal; thus, our data indicate that AIP1 cooperates with ALG-2 in executing the calcium-dependent requirements along the cell death pathway.     

NRP/B, a novel nuclear matrix protein, associates with p110(RB) and is involved in neuronal differentiation

The nuclear matrix is defined as the insoluble framework of the nucleus and has been implicated in the regulation of gene expression, the cell cycle, and nuclear structural integrity via linkage to intermediate filaments of the cytoskeleton. We have discovered a novel nuclear matrix protein, NRP/B (nuclear restricted protein/brain), which contains two major structural elements: a BTB domain-like structure in the predicted NH2 terminus, and a "kelch motif" in the predicted COOH-terminal domain. NRP/B mRNA (5.5 kb) is predominantly expressed in human fetal and adult brain with minor expression in kidney and pancreas. During mouse embryogenesis, NRP/B mRNA expression is upregulated in the nervous system. The NRP/B protein is expressed in rat primary hippocampal neurons, but not in primary astrocytes. NRP/B expression was upregulated during the differentiation of murine Neuro 2A and human SH-SY5Y neuroblastoma cells. Overexpression of NRP/B in these cells augmented neuronal process formation. Treatment with antisense NRP/B oligodeoxynucleotides inhibited the neurite development of rat primary hippocampal neurons as well as the neuronal process formation during neuronal differentiation of PC-12 cells. Since the hypophosphorylated form of retinoblastoma protein (p110(RB)) is found to be associated with the nuclear matrix and overexpression of p110(RB) induces neuronal differentiation, we investigated whether NRP/B is associated with p110(RB). Both in vivo and in vitro experiments demonstrate that NRP/B can be phosphorylated and can bind to the functionally active hypophosphorylated form of the p110(RB) during neuronal differentiation of SH-SY5Y neuroblastoma cells induced by retinoic acid. Our studies indicate that NRP/B is a novel nuclear matrix protein, specifically expressed in primary neurons, that interacts with p110(RB) and participates in the regulation of neuronal process formation.     

Cloning and characterization of RLPK, a novel RSK-related protein kinase

A novel protein kinase whose activity can be stimulated by mitogen in vivo was cloned and characterized. The cDNA of this gene encodes an 802-amino acid protein (termed RLPK) with the highest homology (37% identity) to the two protein kinase families, p90(RSK) and p70(RSK). Like p90(RSR), but not p70(RSK), RLPK also contains two complete nonidentical protein kinase domains. RLPK mRNA is widely expressed in all human tissues examined and is enriched in the brain, heart, and placenta. In HeLa cells, transiently expressed epitope-tagged RLPK can be strongly induced by epidermal growth factor, serum, and phorbol 12-myristate 13-acetate, but only moderately up-regulated by tumor necrosis factor-alpha and other stress-related stimuli. The activity of RLPK stimulated by epidermal growth factor was not inhibited by several known protein kinase C inhibitors nor by rapamycin, a known specific inhibitor for p70(RSK), but could be inhibited by herbimycin A, a tyrosine kinase inhibitor, and partially inhibited by PD98059 or SB203580, inhibitors for the mitogen-activated protein kinase pathways. Recombinant RLPK possesses high phosphorylation activity toward histone 2B and the S6 peptide, RRRLSSLRA. Although purified recombinant RLPK can be phosphorylated by ERK2 and p38alpha in vitro, its activity is not affected by this phosphorylation. Moreover, the treatment of RLPK with acid phosphatase did not reduce its in vitro kinase activity. These data suggest that RLPK is structurally similar to previously isolated RSKs, but its regulatory mechanism may be distinct from either p70(RSK) or p90(RSK)s.     

Cloning and characterization of a cDNA encoding a novel heterogeneous nuclear ribonucleoprotein-like protein and its expression in myeloid leukemia cells

Breast cancer is the second leading cause of cancer-related deaths among women in the United States. Approximately 180,000 new cases of breast cancer are diagnosed each year and a quarter of these are fatal. Early detection is a key to survival of these patients. Unfortunately, no definitive markers are available to diagnose breast cancer at early stages. Identification of such early markers, therefore, is an important priority in breast cancer research. In order to identify early markers, we have focussed on understanding the molecular mechanisms that can lead to conversion of the normal mammary epithelial cells into precancerous immortal cells. Over last several years, we have developed in vitro models of human mammary epithelial cell immortalization which have allowed us to invoke the critical roles of the known tumor suppressor pathways in the maintenance of the untransformed state of mammary epithelial cells. These models are now being used to identify novel genes whose expression is important for normal mammary epithelial cell growth and whose altered expression contributes to breast cell transformation. Characterization of the molecular machinery whose alterations result in early preneoplastic transformation should help identify candidate genes for evaluation as potential early diagnostic markers.     

Structure-based design of a dimeric zinc finger protein

In 1996, the dominant (43%) strain of vancomycin-resistant enterococci (VRE; type A) at Massachusetts General Hospital was identified at Brigham and Women's Hospital (BWH). To characterize the epidemiology of infection with type A isolates of VRE at BWH, we collected demographic and clinical data for all patients from whom VRE were isolated from a clinical specimen through September 1996. The first clinical isolates from all BWH patients from whom VRE were isolated were typed by pulsed-field gel electrophoresis of SmaI digests of chromosomal DNA. Among patients hospitalized after the first patient at BWH infected with a type A isolate of VRE was identified, exposures were compared between patients who acquired type A isolates of VRE and those who acquired other types of VRE. Isolates from 99 patients identified to have acquired VRE were most commonly from blood (n = 27), urine (n = 19), or wounds (n = 19). Three months after the index patient arrived at BWH and at a time when > or =12 types of strains of VRE were present, type A isolates of VRE became dominant; 39 of 75 (52%) of the study cohort had acquired type A isolates of VRE. We found no association between the acquisition of type A isolates of VRE and transfer from another institution or temporal overlap by service, ward, or floor with patients known to have acquired type A isolates of VRE. By multivariate analysis, only residence in the medical intensive care unit (adjusted odds ratio [OR], 3.2; 95% confidence interval [CI], 1.4 to 107) and the receipt of two or more antibiotics per patient-day (adjusted OR, 12.2; 95% CI, 1.2 to 9.0) were associated with the acquisition of strain A. This strain of VRE, dominant at two Boston hospitals, was associated with intensity of antibiotic exposures (i.e., two or more antibiotics per patient-day). We hypothesize that this strain may have unidentified properties providing a mechanism favoring its spread and dominance over other extant isolates, and further studies are needed to define these properties.     

Cloning and characterization of a novel membrane-associated antigenic protein of Helicobacter pylori

BACKGROUND: The aim of this study was to evaluate the effect of convective [hemodiafiltration (HDF) or hemofiltration (HF)] versus diffusive treatments [hemodialysis (HD)] on end-stage renal disease (ESRD) patient mortality and dialysis-related amyloidosis (DRA) using data from the Lombardy Registry. METHODS: For this purpose, 6, 444 patients (aged 56.4 +/- 15.6 years, females 39.5%, diabetics 10. 6%) who started renal replacement therapy (RRT) on HD, HDF, or HF between 1983 and 1995 were considered. A total of 1,082 patients were treated with HDF or HF (first choice in the case of 188), with a median follow-up of 29.7 months. The median follow-up of the 6,298 patients on HD (first choice in the case of 6256) was 22.4 months. The time of survival on dialysis to carpal tunnel syndrome (CTS) surgery was evaluated as a hard marker of DRA morbidity. Survival was compared by means of the Cox proportional regression hazards model, using CTS surgery and all deaths as events for morbidity and mortality, respectively. Explanatory covariates were age, gender, and comorbidities; dialysis modality was tested as a time-dependent covariate. RESULTS: The relative risk (RR) for CTS surgery was significantly higher in older patients [RR = 1.04 per year of age on admission to RRT, 95% confidence interval (CI) 1.02 to 1.06; P = 0. 0001], in diabetics (RR = 2.63, 95% CI 1.30 to 5.31; P = 0.0007), and in patients with heart disease (RR = 5.36, 95% CI 2.27 to 12.68 P = 0.0001). Adjusting for age and diabetic status, the RR for CTS surgery was 42% lower in the patients treated with HDF or HF (RR = 0. 58, 95% CI 0.35 to 0.95, P = 0.03). The RR for mortality, adjusted for age, gender, and comorbidities, was 10% lower in patients treated with HDF or HF (RR = 0.90, 95% CI 0.76 to 1.06; P = NS). CONCLUSION: These results support the hypothesis that convective treatments are associated with a nonsignificant trend toward better survival and significantly delay the need for CTS surgery. An older age and the presence of diabetes and heart disease are other important risk factors for CTS surgery. These results could have an important clinical impact given the relevance of DRA in dialysis patient morbidity.     

Molecular cloning of SKAP55, a novel protein that associates with the protein tyrosine kinase p59fyn in human T-lymphocytes

In human T-lymphocytes the Src family protein tyrosine kinase p59(fyn) associates with three phosphoproteins of 43, 55, and 85 kDa (pp43, pp55, and pp85). Employing a GST-Fyn-Src homology 2 (SH2) domain fusion protein pp55 was purified from lysates of Jurkat T-cells. Molecular cloning of the pp55 cDNA reveals that the pp55 gene codes for a so far nondescribed polypeptide of 359 amino acids that comprises a pleckstrin homology domain, a C-terminal SH3 domain, as well as several potential tyrosine phosphorylation sites, among which one fulfills the criteria to bind Src-like SH2 domains with high affinity. Consistent with this observation, pp55 selectively binds to isolated SH2 domains of Lck, Lyn, Src, and Fyn but not to the SH2 domains of ZAP70, Syk, Shc, SLP-76, Grb2, phosphatidylinositol 3-kinase, and c-abl in vitro. Based on these properties the protein was termed SKAP55 (src kinase-associated phosphoprotein of 55 kDa). Northern blot analysis shows that SKAP55 mRNA is preferentially expressed in lymphatic tissues. SKAP55 is detected in resting human T-lymphocytes as a constitutively tyrosine phosphorylated protein that selectively interacts with p59(fyn). These data suggest that SKAP55 represents a novel adaptor protein likely involved in Fyn-mediated signaling in human T-lymphocytes.     

Characterization and expression of a new class of zinc finger protein that binds to silencer region of ascorbate oxidase gene

A unique A/T-rich sequence (5'-AAAAAGTAAAAA-GTAAAAAAGTAAAAAG-3), referred to as the AGTA repeat, is found in the silencer region of the pumpkin ascorbate oxidase gene. A cDNA for protein (AOBP) that binds to the AGTA repeat was isolated from pumpkin by the southwestern method. The AOBP protein has a new class of zinc/DNA-binding domain named Dof/MOA domain that is highly conserved in many plant proteins and is significantly related to those of steroid hormone receptors and GATA1. Gel retardation analysis indicated that AOBP bound to the AGTA repeat through the Dof/MOA domain. Metal chelators, 1,10-phenanthroline and EDTA, specifically inhibited the DNA binding of AOBP, indicating that metal coordination plays an important role in DNA binding of AOBP. Thus, the Dof/MOA domain acts as a zinc/DNA-binding domain in AOBP. Gel retardation analysis with mutated oligonucleotides suggested that the Dof/MOA domain recognized the AGTA core sequence. AOBP mRNA was expressed in mature tissues of pumpkin, but was expressed only in small amounts or was not expressed in growing tissues. Furthermore, the expression was auxin-independent. The expression pattern of AOBP and that of ascorbate oxidase did not show a positive correlation.     

Cloning and characterization of BAP3 (BAI-associated protein 3), a C2 domain-containing protein that interacts with BAI1

BAI1 (brain-specific angiogenesis inhibitor 1), a p53-target gene specifically expressed in brain, encodes a seven-span transmembrane protein considered to be a member of the secretin receptor family. Using a two-hybrid system, we isolated a cDNA encoding a product that interacts with the cytoplasmic region of BAI1 and designated it BAP3 (BAI1-associated protein 3). The BAP3 product is a novel C2 domain-containing molecule with homology to Munc13 and synaptotagmin. As with Munc13, BAP3 is expressed predominantly in brain. Deletion-mutant analysis revealed that the interaction between BAI1 and BAP3 was not mediated by the C2 domains. Its predominant expression in brain and homology to Munc13 indicate that BAP3, by interacting with BAI1, might be involved in some neuronal function such as regulating release of neurotransmitters.     

Identification of a novel MCM3-associated protein that facilitates MCM3 nuclear localization

MCM3 is essential for the initiation of DNA replication and also participates in controls that ensure DNA replication is initiated once per cell cycle. In a two-hybrid screen for proteins that interact with human MCM3, we identified and cloned a novel protein of which the calculated molecular weight is 80,291. A specific antibody against the protein identified a 80-kDa protein in HeLa cell extract, indicating the protein actually expressed in cells. The interaction of these proteins was confirmed by immunoprecipitation assay. Moreover, we clarified a nuclear localization signal of human MCM3, and we find that mutagenesis on the nuclear localization signal of MCM3 affected the binding of newly isolated MCM3-assosiated protein, Map80. Map80 was expressed in Escherichia coli as a fusion with His6 tag and purified with sequential column chromatographies. The addition of recombinant Map80 stimulated the amount of nuclear localized MCM3. These results suggest that Map80 is involved in the nuclear localization pathway of MCM3.