Signal Sequence Trap Method Research Articles

Isolation and Characterization of CA XIV, a Novel Membrane-bound Carbonic Anhydrase from Mouse Kidney

Carbonic anhydrase (CA) is involved in various physiological processes such as acid-base balance and transport of carbon dioxide and ions. In this study, we have succeeded in the isolation of a novel CA from the mouse kidney by use of the signal sequence trap method. It is a 337-amino acid polypeptide with a calculated molecular mass of 37.5 kDa, consisting of a putative amino-terminal signal sequence, a CA domain, a transmembrane domain, and a short hydrophilic carboxyl terminus, which we designated CA XIV. The CA domain of CA XIV is highly homologous with those of known CAs, especially extracellular CAs including CA XII, IX, VI, and IV. The expression study of an epitope-tagged protein has suggested that CA XIV is located on the plasma membrane. When expressed in COS-7 cells, CA XIV exhibits CA activity that is predominantly associated with the membrane fraction. By Northern blot analysis, the gene expression of CA XIV is most abundant in the kidney and heart, followed by the skeletal muscle, brain, lung, and liver. In situ hybridization has revealed that, in the kidney, the gene is expressed intensely in the proximal convoluted tubule, which is the major segment for bicarbonate reabsorption and also in the outer border of the inner stripe of the outer medulla. In conclusion, we have cloned a functional cDNA encoding a novel membrane-bound CA. This study will bring new insights into our understanding of carbon dioxide metabolism and acid-base balance.

Trapping cDNAs encoding secreted proteins from the salivary glands of the malaria vector Anopheles gambiae.

The signal sequence trap method was used to isolate cDNAs corresponding to proteins containing secretory leader peptides and whose genes are expressed specifically in the salivary glands of the malaria vector Anopheles gambiae. Fifteen unique cDNA fragments, ranging in size from 150 to 550 bp, were isolated and sequenced in a first round of immunoscreening in COS-7 cells. All but one of the cDNAs contained putative signal sequences at their 5' ends, suggesting that they were likely to encode secreted or transmembrane proteins. Expression analysis by reverse transcription-PCR showed that at least six cDNA fragments were expressed specifically in the salivary glands. Fragments showing a high degree of similarity to D7 and apyrase, two salivary gland-specific genes previously found in Aedes aegypti, were identified. Of interest, three different D7-related cDNAs that are likely to represent a new gene family were found in An. gambiae. Moreover, three salivary gland-specific cDNA fragments that do not show similarity to known proteins in the databases were identified, and the corresponding full length cDNAs were cloned and sequenced. RNA in situ hybridization to whole female salivary glands showed patterns of expression that overlap only in part those observed in the culicine mosquito A. aegypti.

27] The signal sequence trap method

This chapter discusses the signal sequence trap method. The signal sequence trap method serve to identify secreted proteins, type 1 and type 2 transmembrane proteins, proteins with multiple membrane-spanning regions, glycosyl-phosphatidylinositol (GPI)-anchored proteins, and proteins in the endoplasmic reticulum (ER), Golgi apparatus (GA), lysosomes, and other reticular structures downstream of the ER. Many trials to isolate those molecules have been performed using not only the original Tac(3')-COS7 reporter system, but also other reporter proteins and host cells such as CD4 without the signal sequence, the protease domain of urokinase-type plasminogen activator, and yeast invertase. Each generic system has some advantages and disadvantages. With the yeast system, more clones can be trapped in a short period. Each system has its own biases in the kinds of proteins trapped, because each reporter system and host cells have some preferences in the kinds of proteins allowed to enter the ER, although in every system, short fragments of DNAs without hydrophobic regions are trapped for unknown reasons. So long as reasonable-length DNAs are tested, the signal sequence trap method is a potent tool for identifying surface markers and intercellular signal-transducing proteins.

Molecular Cloning, Characterization, and Chromosomal Localization of FKBP23, a Novel FK506-Binding Protein with Ca2+-Binding Ability

We have identified and characterized a cDNA encoding a novel FK506-binding protein (FKBP), named FKBP23, from mouse heart by the signal sequence trap method. The deduced amino acid sequence has significant homology to other FKBP family members around the peptidylprolylcis-trans-isomerase motifs. FKBP23 also has two Ca2+-binding (EF-hand) motifs, and purified FKBP23 protein was shown to have Ca2+-binding ability. This is the first report of a Ca2+-binding FKBP. FKBP23 is a glycoprotein retained in the endoplasmic reticulum by its carboxyl-terminal tetrapeptide His-Asp-Glu-Leu, as demonstrated by immunostaining, retention, and deglycosylation assays. FKBP23 mRNA is expressed most strongly in heart, lung, and testis, beginning at day 8.5 of embryonic development. The FKBP23 gene was mapped to mouse chromosome 2.

Entactin-2: A New Member of Basement Membrane Protein with High Homology to Entactin/Nidogen

Using the new signal sequence trap (SST) method, we isolated several clones encoding secreted and transmembrane proteins from KUSA cells, a murine osteoblast-like cell line. One isolated novel clone, termed entactin-2, exhibited a high similarity to mouse entactin/nidogen, a basement membrane protein. Although deduction of the amino acid sequence of entactin-2 revealed only 27.4% homology to entactin, many structural similarities were seen between both proteins. Entactin-2 contains five EGF-like and two thyroglobulin-like motifs, which are both cysteine-rich. Comparison of both proteins clearly revealed that entactin-2 also contains related domain structures. The rod-like domain of entactin-2, containing the RGD integrin recognition sequence, fused to glutathione-Stransferase (GST), revealed a cell surface-binding activity similar to that of entactin. In addition, the tissue distribution of entactin-2 mRNA resembled that of entactin. Furthermore, mRNA expression of both genes decreased as osteoblastic differentiation progressed. These results suggest that entactin-2 is a member of the entactin gene family, may have entactin-related functions, and might act as a basement membrane component.

Identification of a new class of chemokine expressed in murine dendritic cells by the signal sequence trap method

Identification of a new class of chemokine expressed in murine dendritic cells by the signal sequence trap method

Identification of a neutrophil gelatinase-associated lipocalin mRNA in human pancreatic cancers using a modified signal sequence trap method

To identify the intercellular signal-transducing proteins and receptors produced by cancer cells, we attempted to clone cDNAs encoding secreted and type I membrane proteins using a signal sequence trap (SST) method with some modifications. By screening an SST library derived from pancreatic cancer cells, we identified two secretory proteins (neutrophil gelatinase-associated lipocalin (NGAL) and lung surfactant protein D) and three membrane proteins (carcinoembryonic antigen, BiP/GRP78 and Hsa4 mitochondrion cytochrome oxidase subunit II). NGAL mRNA was expressed in eight of the pancreatic cancer cell lines and eight pancreatic cancer tissues. The expression of NGAL mRNA was also observed in colorectal and hepatic tumors.

Kidney-specific expression of a novel mouse organic cation transporter-like protein

Using the signal sequence trap method, we have cloned a novel 12-membrane-spanning transporter-like protein, termed renal-specific transporter (RST), from the mouse kidney. RST is a 553-amino-acid protein highly homologous to recently cloned organic cation transporters, e.g. it is 30% identical to rat organic cation transporter 1 at the amino acid level. Northern blot analysis has revealed that the RST gene is expressed abundantly and specifically in the kidney. In situ hybridization analysis has shown that RST gene expression is restricted to the renal proximal tubule, where various organic cations such as endogenous catecholamines and choline or clinically used cationic drugs are known to be actively excreted.

Calumenin, a Ca2+-binding protein retained in the endoplasmic reticulum with a novel carboxyl-terminal sequence, HDEF.

We have identified and characterized a cDNA encoding a novel Ca2+-binding protein named calumenin from mouse heart by the signal sequence trap method. The deduced amino acid sequence (315 residues) of calumenin contains an amino-terminal signal sequence and six Ca2+-binding (EF-hand) motifs and shows homology with reticulocalbin, Erc-55, and Cab45. These proteins seem to form a new subset of the EF-hand protein family expressed in the lumen of the endoplasmic reticulum (ER) and Golgi apparatus. Purified calumenin had Ca2+-binding ability. The carboxyl-terminal tetrapeptide His-Asp-Glu-Phe was shown to be responsible for retention of calumenin in ER by the retention assay, immunostaining with a confocal laser microscope, and the deglycosylation assay. This is the first report indicating that the Phe residue is included in the ER retention signal. Calumenin is expressed most strongly in heart of adult and 18.5-day embryos. The calumenin gene (Calu) was mapped at the proximal portion of mouse chromosome 7.

Molecular cloning of a novel mouse aspartic protease-like protein that is expressed abundantly in the kidney

By use of the signal sequence trap method, we isolated a cDNA encoding a novel aspartic protease-like protein from the mouse kidney, and termed it `kidney-derived aspartic protease-like protein (KAP).' The protein, a 419-amino-acid polypeptide with a 16-amino-acid signal sequence, had 47% identity with mouse cathepsin D, and its overall structure was closely related to known aspartic proteases. Northern blot analysis revealed that KAP mRNA is expressed at the highest level in the kidney, at a moderate level in the lung, and at low levels in the spleen and adipose tissue. In situ hybridization analysis demonstrated that the mRNA is expressed abundantly in the proximal straight tubule and slightly, but significantly, in the proximal convoluted tubule in the kidney. This intra-renal distribution differs distinctly from those of previously reported proteases such as cathepsins B, D, and H.

Characterization of Novel Secreted and Membrane Proteins Isolated by the Signal Sequence Trap Method

We recently described a method, called the signal sequence trap (SST) method, to clone cDNAs of secreted proteins and/or type I transmembrane proteins containing N-terminal signal sequences by using an epitope-tagging expression plasmid vector. In this paper we describe the summary of a large-scale screening of approximately 5900 clones of an SST cDNA library constructed from mouse bone marrow stromal cell line ST-2 cells. Of 26 positive clones obtained and sequenced, 11 clones appeared to contain authentic signal sequences. Five of the clones corresponded to the 5′ ends of the cDNA of known genes containing N-terminal signal sequences. The full-length cDNA clones of the 6 other unknown clones were isolated and sequenced. One clone, termed SDF3, encoded a mouse counterpart of human pigment epithelium-derived factor. Another clone, termed SDR1, had considerable homology with basigin, a member of the immunoglobulin superfamily. A third clone, termed SDF5, had partial homology with aDrosophilatissue polarity genefrizzled(fz) and its rat homologues,fz-1andfz-2.The other three clones had no significant homology with sequences in the databases. These results indicate that the SST method is effective and useful for the isolation of secreted and membrane proteins without knowledge of their functions.

Isolation and characterization of a novel secretory protein, stromal cell-derived factor-2 (SDF-2) using the signal sequence trap method

With use of the signal sequence trap method, we isolated a cDNA encoding a novel secretory protein, SDF-2, from the mouse stromal cell line, ST2. The human homologue of SDF-2 was also isolated. The amino acid (aa) sequences deduced from both the clones were conserved more than 92%. The chromosomal localization of the human SDF-2 gene was mapped to 17q11.2. The aa sequence of SDF-2 shows similarity to those of yeast dolichyl phosphate- d-mannose:protein mannosyltransferases, Pmtlp [Strahl-Bolsinger et al. (1993) Proc. Natl. Acad. Sci. USA 90, 8164-8168] and Pmt2p [Lussier et al. (1995) J. Biol. Chem. 270, 2770-2775], whose activities have not been detected in higher eukaryotes.

Molecular Cloning of a Novel T Cell-directed CC Chemokine Expressed in Thymus by Signal Sequence Trap Using Epstein-Barr Virus Vector

Precursors of most secreted and cell surface molecules carry signal sequences at their amino termini. Here we describe an efficient signal sequence trap method and isolation of a novel CC chemokine. An expression library was constructed by inserting 5' portion-enriched cDNAs from phytohemagglutinin-stimulated peripheral blood mononuclear cells into upstream of signal sequence-deleted CD4 cDNA in an Epstein-Barr virus shuttle vector. After electroporation into Raji cells, CD4 antigen-positive cells were enriched by repeated cell sorting and plasmids were recovered in Escherichia coli. Out of 100 plasmid clones examined, 42 clones directed expression of CD4 antigen on the cell surface. Among them were signal sequences of CD6, beta2-microglobulin, MGC-24, and T cell receptor epsilon-chain, and at least four novel potential signal sequences. A cDNA clone encoding a novel CC chemokine was isolated by using one of the trapped fragments. The gene designated as TARC from Thymus and Activation-Regulated Chemokine was expressed transiently in phytohemagglutinin-stimulated peripheral blood mononuclear cells and constitutively in thymus. Radiolabeled recombinant TARC specifically bound to T cell lines and peripheral T cells but not to monocytes or granulocytes. The binding of radiolabeled TARC to the high-affinity receptor (Kd, 2.1 nM) on Jurkat was displaced by TARC but not by interleukin-8, MIP-1alpha, RANTES, or MCP-1. TARC also bound to the promiscuous chemokine receptor on erythrocytes (Kd, 17 nM). TARC induced chemotaxis in T cell lines Hut78 and Hut102. Pretreatment of Hut78 with pertussis toxin abolished the TARC-induced cell migration. Collectively, T cells express a highly selective receptor for TARC that is coupled to pertussis toxin-sensitive G-protein. TARC may a factor playing important roles in T cell development in thymus as well as in trafficking and activation of mature T cells.

The Murine Lymphotoxin-β Receptor cDNA: Isolation by the Signal Sequence Trap and Chromosomal Mapping

To isolate novel molecules involved in intercellular signaling during mouse embryogenesis, we employed the signal sequence trap (SST) method, a newly developed strategy for cloning secreted proteins and type I membrane proteins. We constructed an SST cDNA library of mouse embryonic heart mRNA, screened 2000 clones, and acquired 1 positive clone that appeared to contain the signal sequence. Homology searches revealed that this clone encodes the mouse lymphotoxin-β receptor (LTβ-R). The deduced amino acid sequence of the mouse LTβ-R was 66% identical to that of the human LTβ-R. Northern analysis of various organs in adult mice showed that expression levels of LTβ-R mRNA were strong in lung, liver, and kidney, moderate in heart and testis, but weak in brain, thymus, spleen, and lymph nodes. Since the mouse LTβ-R was already expressed in 7-day-postcoitus embryo, the LTβ/LTβ-R system might have some functions in early embryogenesis. We performed chromosomal mapping of the murine LTβ-R gene by linkage analysis with recombinant inbred mouse strains and found that its locus is very close to the tumor necrosis factor receptor 1 gene on chromosome 6.

Structure and Chromosomal Localization of the Human Stromal Cell-Derived Factor 1 (SDF1) Gene

Stromal cell-derived factors 1α and 1β are small cytokines belonging to the intercrine CXC subfamily and originally isolated from a murine bone-marrow stroma cell line by the signal sequence trap method. cDNA and genomic clones of human SDF1α and SDF1β (SDF1A and SDF1B) were isolated and characterized. cDNAs of SDF1α and SDF1β encode proteins of 89 and 93 amino acids, respectively. SDF1α and SDF1β sequences are more than 92% identical to those of the human counterparts. The genomic structure of the SDF1 gene revealed that human SDF1α and SDF1β are encoded by a single gene and arise by alternative splicing. SDF1α and SDF1β are encoded by 3 and 4 exons, respectively. Ubiquitous expression of the SDF1 gene, except in blood cells, was consistent with the presence of the GC-rich sequence in the 5′-flanking region of the SDF1 gene, as is often the case in the "housekeeping" genes. Although genes encoding other members of the intercrine family are localized on chromosome 4q or 17q, the human SDF1 gene was mapped to chromosome 10q by fluorescence in situ hybridization. Strong evolutionary conservation and unique chromosomal localization of the SDF1 gene suggest that SDF1α and SDF1β may have important functions distinct from those of other members of the intercrine family.