Sequence analysis of a salt tolerant metagenomic clone

Metagenome represent an unlimited resource for discovery of novel genes. Here we report, sequence analysis of a salt tolerant metagenomic clone (6B4) from a pond water metagenomic library. Clone 6B4 had an insert of 2254 bp with G+C composition of 64.06%. DNA sequence from 6B4 showed homology to DNA sequences from pro-teobacteria indicating origin of 6B4 metagenomic insert from a yet uncharacterized proteobacteria. Two encoded proteins from clone 6B4 showed match with ATP-depen-dent Clp protease adaptor protein (ClpS) and phasin, while two truncated encoded proteins showed match with poly-3-hydroxybutyrate synthase and permease. Clp complex is known to play a role in stress tolerance. Expression of ClpS from metagenomic clone is proposed to be responsible for salt tolerance of the metagenomic clone 6B4.     

Evolution of a carbohydrate binding module into a protein-specific binder

A carbohydrate binding module, CBM4-2, derived from the xylanase (Xyn 10A) of Rhodothermus marinus has been used as a scaffold for molecular diversification. Its binding specificity has been evolved to recognise a quite different target, a human monoclonal IgG4. In order to understand the basis for this drastic change in specificity we have further investigated the target recognition of the IgG4-specific CBMs. Firstly, we defined that the structure target recognised by the selected CBM-variants was the protein and not the carbohydrates attached to the glycoprotein. We also identified key residues involved in the new specificity and/or responsible for the swap in specificity, from xylan to human IgG4. Specific changes present in all these CBMs included mutations not introduced in the design of the library from which the specific clones were selected. Reversion of such mutations led to a complete loss of binding to the target molecule, suggesting that they are critical for the recognition of human IgG4. Together with the mutations introduced at will, they had transformed the CBM scaffold into a protein binder. We have thus shown that the scaffold of CBM4-2 is able to harbour molecular recognition for either carbohydrate or protein structures.     

Purification and characterization of a type II phosphatidylinositol 4-kinase from rat spleen and comparison with a PtdIns 4-kinase from lymphocytes.

A PtdIns 4-kinase from rat spleen particulate fraction was purified to homogeneity and its molecular properties were compared with a PtdIns 4-kinase from splenic lymphocytes. The enzyme activity was solubilized from spleen particulate fraction with Triton X-100 and chromatographed sequentially on phosphocellulose, DEAE-sephacel, heparin acrylamide and hydroxyapatite columns. The purified enzyme preparation showed a 55 kDa band on SDS-PAGE with silver staining. Renaturation of the enzyme activity from SDS-PAGE showed that it comigrated with the 55 kDa protein. Characterization of the enzyme showed that it was a type II PtdIns 4-kinase. Polyclonal antibodies raised against PtdIns 4-kinase inhibited the enzyme activity in in vitro assays. Analysis of adult rat tissue particulate fractions on immunoblots showed restricted immunoreactivity among PtdIns 4-kinases. However, the immunoreactivity is conserved in lymphoid tissues from mouse to human, suggesting that lymphoid tissue has a distinct PtdIns 4-kinase. Activation of rat splenocytes with Con A showed two fold increase in PtdIns 4-kinase activity. Comparison of PtdIns 4-kinases from spleen and splenic lymphocytes showed identical chromatographic behaviour, molecular mass, immunoreactivity, K(m) values for PtdIns and inhibition by adenosine.     

Eukaryotic initiation factor 4B from wheat and Arabidopsis thaliana is a member of a multigene family

Clones of eukaryotic initiation factor (eIF) 4B from wheat and Arabidopsis thaliana were obtained from cDNA and genomic libraries. The exon/intron organization of the genes from wheat and A. thaliana is very similar. The deduced amino acid sequences for the wheat and Arabidopsis eIF4B proteins showed overall similarity to each other, but very little similarity to eIF4B from other eukaryotes. The recombinant form of eIF4B supports polypeptide synthesis in an in vitro translation system and reacts with antibodies to native wheat eIF4B. In contrast to mammalian eIF4B and eIF4A, the combination of wheat eIF4B and eIF4A does not stimulate RNA-dependent ATP hydrolysis activity; however, wheat eIF4B does stimulate eIF4F and eIF4A RNA-dependent ATP hydrolysis activity. Interestingly, eIF4B does not stimulate eIF(iso)4F and eIF4A hydrolysis activity. Gel filtration experiments indicate wheat eIF4B, like its mammalian counterpart, self-associates to form a homodimer.     

Molecular cytogenetic characterization of ring chromosome 4 in a female having a chromosomally normal child

We present the clinical and molecular findings of mosaic ring chromosome 4. The patient was referred to us for infertility and short stature. Results of three repeated cytogenetic analyses from lymphocytes showed a similar mosaic karyotype with multiple cell-lines [46,XX,r(4)/45,XX,-4/46,XX,dic r(4)/47,XX,r(4),+r(4)/46,XX]. FISH showed deletion of the 4p subtelomeric region and the 4q telomeric region from the ring chromosome 4. The breakpoints were mapped using molecular analysis. Parental karyotypes were normal. During the course of this study, the patient became pregnant without assisted reproductive technology. The result of amniocentesis performed at 16 weeks gestation showed a normal karyotype. Delivery was uncomplicated. This is the first report, to our knowledge, of the presence of ring chromosome 4 having various mosaic conditions in a female having a chromosomally normal fetus.     

Schizosaccharomyces pombe isp4 encodes a transporter representing a novel family of oligopeptide transporters

We have recently cloned an oligopeptide transport gene from Candida albicans denoted OPT1 . This gene showed significant sequence similarity to three open reading frames (ORFs) with no previously established function: isp4 from Schizosaccharomyces pombe and Saccharomyces cerevisiae YJL212C and YPR194C , identified during the genome project. The S . pombe gene isp4 was originally identified by Sato et al . as a gene that was upregulated through nitrogen starvation induction of meiosis. However, an isp4Δ strain exhibited a wild-type phenotype with respect to sexual differentiation. We have found that the same isp4Δ strain is deficient in tetrapeptide transport activity as measured by its resistance to toxic tetrapeptides, by its inability to accumulate a radiolabelled tetrapeptide and by the inability to use tetrapeptides as a sole source of an amino acid to satisfy an auxotrophic requirement. Similarly, we found that the ORF YPR194C from S . cerevisiae encodes an oligopeptide transporter. Sequence analyses as well as physiological evidence has led us to propose that the proteins encoded by isp4 and the genes identified from S . cerevisiae and C . albicans comprise a new group of transporters specific for small oligopeptides, which we have named the OPT family.     

FGFR-4, a novel acidic fibroblast growth factor receptor with a distinct expression pattern.

We have previously identified two novel members of the fibroblast growth factor receptor (FGFR) gene family expressed in K562 erythroleukemia cells. Here we report cDNA cloning and analysis of one of these genes, named FGFR-4. The deduced amino acid sequence of FGFR-4 is 55% identical with both previously characterized FGFRs, flg and bek, and has the structural characteristics of a FGFR family member including three immunoglobulin-like domains in its extracellular part. Antibodies raised against the carboxy terminus of FGFR-4 detected 95 and 110 kd glycoproteins with a protein backbone of 88 kd in COS cells transfected with a FGFR-4 cDNA expression vector. The FGFR-4 protein expressed in COS cells could also be affinity-labeled with radioiodinated acidic FGF. Furthermore, ligand binding experiments demonstrated that FGFR-4 binds acidic FGF with high affinity but does not bind basic FGF. FGFR-4 is expressed as a 3.0 kb mRNA in the adrenal, lung, kidney, liver, pancreas, intestine, striated muscle and spleen tissues of human fetuses. The expression pattern of FGFR-4 is distinct from that of flg and bek and the yet additional member of the same gene family, FGFR-3, which we have also cloned from the K562 leukemia cells. Our results suggest that FGFR-4 along with other fibroblast growth factor receptors performs cell lineage and tissue-specific functions.     

A plant Y chromosome-STS marker encoding a degenerate retrotransposon

The dioecious plant Silene latifolia has both X and Y sex chromosomes. Male-specific random amplified polymorphic DNA (RAPD) fragments were analyzed to identify Y-chromosome-linked sequences. One of the RAPD fragments, MS4, was converted into a more reliable and reproducible sequence-tagged site (STS) marker. A set of MS4 STS primers was used to amplify two genomic DNA fragments (MS4a and MS4b) from a male plant and one (MS4a) from a female plant, which indicates that MS4b is located on the Y chromosome. Sequence analysis revealed that MS4a encoded a gag protein of a Ty3-gypsy-like retrotransposon. A 147-bp region from the middle of MS4a was deleted in MS4b. The MS4b sequence was not detected in the most closely related dioecious species, S. dioica. This suggests that a retrotransposon with the MS4b sequence has degenerated recently on the Y chromosome.     

Stage-specific induction of terminal deoxynucleotidyl transferase in a T-lymphoid line upon coculture with a thymic stromal line

We previously reported an in vitro T-cell differentiation system in which the L4 lymphoid clone was cocultured with the St3 stromal line derived from the same murine thymic tumor, 15#4T. L4 cells in L4—St3 cocultures sequentially express Thy-1 and CD4 in a manner typical of normal thymocytes. In contrast, L4 cells grown in medium alone retain their Thy-1⁻CD4⁻ phenotype. We also isolated L4 subclones from the coculture with increasingly differentiated phenotypes with respect to Thy-1 and CD4. We now report induction of an additional thymocyte differentiation marker, terminal deoxynucleotidyl transferase (TdT) in 15#4T cells (and to a lesser extent subcloned L4 cells) upon coculture with St3 stroma. Coculture of 15#4T cells with St3 stroma resulted in expression of TdT as measured by ribonuclease protection for TdT RNA and Western immunoblotting for TdT protein. Cocultured L4 cells were induced for TdT expression to a lesser degree and for a shorter period of time. The magnitude of TdT RNA induction was maximal for cell lines with the least mature differentiation phenotype (15#4T and L4: Thy-1⁻CD4⁻) and decreased proportionally for subclones with increasingly mature phenotype, e.g., L4E cells (Thy-1⁺CD4⁺). TdT protein was undetectable by Western immunoblotting and immunofluorescent staining of the L4E subclone on or off stroma. Recombination-activating gene-1 (RAG-1), which is expressed in immature thymocytes during T-cell receptor rearrangement, but suppressed in mature thymocytes, was also examined using the ribonuclease protection assay. In contrast to TdT, RAG-1 expression was suppressed by coculture with St3 cells for 15#4T and also more mature subclones, indicating regulation by a mechanism independent from TdT. The ordered induction of TdT, Thy-1, and CD4, as well as regulation of RAG-1 in the 15#4T-St3 system, supports the conclusion that this in vitro system is a valuable model for characterizing regulation of these markers in normal thymocytes.     

Identification of a T cell subset using a rabbit antibody raised against a T suppressor molecule

Rabbit antiserum to a unique component of an Ag-binding Ts-factor was generated by repeated immunization with purified 30-kDa protein isolated from Fd11 Ts factor (11). This antiserum (anti-p30) was shown to recognize cell surface determinants expressed on the Ts hybridomas Fd11 and A10 but not the fusion partner BW5147. Furthermore, this antiserum was shown to bind to approximately 4% of thymocytes and 10% of nylon wool-purified splenic T cells from all strains of mice tested. Sorting nylon wool-purified T cells from DBA/2 mice for the CD4+ and CD8+ subsets revealed both populations contained cells that bound anti-p30. In addition, when CD4-8- thymocytes were examined for anti-p30 labeling, it was found that about 30% of this enriched population also expressed p30 molecules. In a functional study, anti-p30 was able to neutralize the suppressive effects of Fd11 on a specific assay for in vitro antibody synthesis against ferredoxin.     

Characterization of a novel allele of glucose oxidase from a Korean wild type strain of Aspergillus niger.

We have identified a novel allele of the glucose oxidase (GO, EC1.1.3.4) gene (GO) from a Korean wild type strain of Aspergillus niger, ACMO4, with an increased GO activity in culture filtrate. Southern blot analyses of GO from ACMO4 (GO-ACMO4) revealed that the gene was present as a single copy in the genome of A. niger. However, its sequence differs from that of GO from A. niger ATCC 9029 (GO-ATCC9029). GO-ACMO4 appears to be a functional gene based on the fact that it is enzymatically active when heterologously expressed in yeast. Sequence comparisons of the coding region of GO-ACMO4 revealed 16 nucleotide changes that resulted in four amino acid substitutions; T432D, G517D, G530S, and Q542R. The GO proteins from both ATCC 9029 and ACMO4 were heterologously expressed, purified, and compared biochemically. The two enzymes showed no difference in their apparent Km value for glucose (30 mM), but the Vmax of GO-ACMO4 (515.6 unit/mg) was 10% higher than that of GO-ATCC 9029, resulting in a 10% higher specific activity.     

Caspase cleavage of initiation factor 4E-binding protein 1 yields a dominant inhibitor of cap-dependent translation and reveals a novel regulatory motif

Eukaryotic initiation factor 4E (eIF4E) binding proteins (4E-BPs) regulate the assembly of initiation complexes required for cap-dependent mRNA translation. 4E-BP1 undergoes insulin-stimulated phosphorylation, resulting in its release from eIF4E, allowing initiation complex assembly. 4E-BP1 undergoes caspase-dependent cleavage in cells undergoing apoptosis. Here we show that cleavage occurs after Asp24, giving rise to the N-terminally truncated polypeptide Delta4E-BP1, which possesses the eIF4E-binding site and all the known phosphorylation sites. Delta4E-BP1 binds to eIF4E and fails to become sufficiently phosphorylated upon insulin stimulation to bring about its release from eIF4E. Therefore, Delta4E-BP1 acts as a potent inhibitor of cap-dependent translation. Using a mutagenesis approach, we identify a novel regulatory motif of four amino acids (RAIP) which lies within the first 24 residues of 4E-BP1 and which is necessary for efficient phosphorylation of 4E-BP1. This motif is conserved among sequences of 4E-BP1 and 4E-BP2 but is absent from 4E-BP3. Insulin increased the phosphorylation of 4E-BP3 but not sufficiently to cause its release from eIF4E. However, a chimeric protein that was generated by replacing the N terminus of 4E-BP3 with the N-terminal sequence of 4E-BP1 (containing this RAIP motif) underwent a higher degree of phosphorylation and was released from eIF4E. This suggests that the N-terminal sequence of 4E-BP1 is required for optimal regulation of 4E-BPs by insulin.     

Identification of a human endothelial cell antigen with monoclonal antibody 44G4 produced against a pre-B leukemic cell line

Staining of a variety of human tissue sections (lymph node, tonsil, spleen, thymus, kidney, lung, and liver) by the indirect immunoperoxidase method indicated that mAb 44G4, produced against a human pre-B leukemic cell line, was strongly reactive with vascular endothelium. All other cell types observed in these tissues were unreactive. Immunofluorescence staining of endothelial cells isolated from umbilical cord vein and grown in culture confirmed that mAb 44G4 recognized a surface membrane component of vascular endothelium. Granulocytes, monocytes, B and T lymphocytes, and T lymphocytes cultured in the presence of PHA for 72 h did not express the 44G4 Ag. mAb 44G4 reacted weakly with leukemic cells from 28 of 41 patients with non-T cell acute lymphocytic leukemia and 4 of 7 patients with acute myelocytic leukemia, whereas 8 of 10 cases of T cell acute lymphocytic leukemia were negative. Moderate reactivity with leukemic cell lines of pre-B and myelomonocytic origin was also observed. The level of 44G4 Ag on umbilical endothelial cells was three to five times that of leukemic cell lines and 25 times the average levels observed on leukemic cells isolated from patients. Immunoprecipitation of lysates prepared from surface-iodinated endothelial cells and the immunizing pre-B leukemic cell line revealed that the 44G4 Ag from both cell types was composed of two subunits of apparent m.w. 95,000 linked by disulfide bond(s). Comparison of the cellular localization and subunit structure of 44G4 to that of known Ag suggests that it represents a previously undescribed marker of endothelial cells.     

An alteration in outer membrane permeability associated with a division lesion in a strain of Salmonella typhimurium.

Salmonella typhimurium strain 4a is a temperature sensitive mutant with defects in both septation and separation. The separation lesion was reversed by phenethylalcohol but this agent failed to allow septation or growth at restrictive temperature. Organisms of strain 4a grown at 42 degrees C were, unlike the parental strain, resistant to lysis by lysozyme plus EDTA and lipopolysaccharide was poorly extracted by EDTA from cultures of strain 4a grown at 42 degrees C. Such cultures may, therefore, be resistant to lysis with lysozyme plus EDTA not because the murein is altered but because the EDTA fails to permeabilize the outer membrane to lysozyme. In confirmation of this, murein isolated from strain 4a after growth at 42 degrees C showed the same sensitivity to lysozyme as murein from the parental strain. In spite of the altered envelope properties of strain 4a after growth at 42 degrees C, no major changes in protein or phospholipid composition have so far been demonstrated.     

Detection of a fourth orbivirus non-structural protein

The genus Orbivirus includes both insect and tick-borne viruses. The orbivirus genome, composed of 10 segments of dsRNA, encodes 7 structural proteins (VP1-VP7) and 3 non-structural proteins (NS1-NS3). An open reading frame (ORF) that spans almost the entire length of genome segment-9 (Seg-9) encodes VP6 (the viral helicase). However, bioinformatic analysis recently identified an overlapping ORF (ORFX) in Seg-9. We show that ORFX encodes a new non-structural protein, identified here as NS4. Western blotting and confocal fluorescence microscopy, using antibodies raised against recombinant NS4 from Bluetongue virus (BTV, which is insect-borne), or Great Island virus (GIV, which is tick-borne), demonstrate that these proteins are synthesised in BTV or GIV infected mammalian cells, respectively. BTV NS4 is also expressed in Culicoides insect cells. NS4 forms aggregates throughout the cytoplasm as well as in the nucleus, consistent with identification of nuclear localisation signals within the NS4 sequence. Bioinformatic analyses indicate that NS4 contains coiled-coils, is related to proteins that bind nucleic acids, or are associated with membranes and shows similarities to nucleolar protein UTP20 (a processome subunit). Recombinant NS4 of GIV protects dsRNA from degradation by endoribonucleases of the RNAse III family, indicating that it interacts with dsRNA. However, BTV NS4, which is only half the putative size of the GIV NS4, did not protect dsRNA from RNAse III cleavage. NS4 of both GIV and BTV protect DNA from degradation by DNAse. NS4 was found to associate with lipid droplets in cells infected with BTV or GIV or transfected with a plasmid expressing NS4.