bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation of guide RNA/messenger RNA chimeric molecules in vitro, the initial step of RNA editing, is dependent on an anchor sequence.
Authors: Blum B , Simpson L
Published: May 2006

Synthetic pre-edited messenger RNA (mRNA) and guide RNA (gRNA) for the 5'-edited maxicircle-encoded ND7 cryptogene from Leishmania tarentolae formed chimeric molecules upon incubation in the presence of a mitochondrial extract. These chimeric molecules consisted of the gRNAs covalently linked to the mRNAs by short oligo(U) tails at normal editing sites in most cases. Unlike the previously reported chimeras present in steady-state kinetoplast RNA, the in vitro-synthesized chimeras showed no editing of downstream editing sites. The synthesis of chimeric RNAs required ATP and was dependent on the formation of a gRNA/mRNA anchor duplex 3' of the pre-edited region, as shown by in vitro mutagenesis of the mRNA and the gRNA. mRNA sequences 3' and 5' of the pre-edited region also affected the efficiency of the chimera-forming activity. This in vitro system may accurately represent the initial step in RNA editing.
Cell cycle-dependent changes in the organization of an intermediate filament-associated protein: correlation with phosphorylation by p34cdc2.
Authors: Skalli O , Chou Y H , Goldman R D
Published: May 2006

During mitosis in BHK-21 baby hamster kidney cells the hyperphosphorylation of the type III intermediate filament (IF) protein vimentin is accompanied by the disruption of the IF network into punctate, protofilamentous structures. In this study, the morphological and biochemical changes of IFAP 300, a 300-kDa IF-crossbridging protein, are examined during mitosis. Double-label immunofluorescence shows that the distribution of IFAP 300 coincides with the typical filamentous pattern displayed by vimentin in interphase cells, whereas in mitotic cells it is reorganized into a punctate, nonfilamentous pattern. Accompanying these latter morphological changes, IFAP 300 is phosphorylated at a unique, mitosis-specific site. Comparison of the sites phosphorylated in cultured cells with those phosphorylated in vitro by various kinases suggests that IFAP 300 is phosphorylated by the same two kinases that phosphorylate vimentin during mitosis. One of these is p34cdc2 protein kinase, which appears to be responsible for the phosphorylation of the mitosis-specific site. The other kinase phosphorylates IFAP 300 in vitro at a site that is also found in the protein immunoprecipitated from either mitotic or interphase cells. In contrast to vimentin, the phosphorylation levels of IFAP 300 are not obviously altered between interphase and mitosis. Our results show that IFAP 300 is a physiological substrate for p34cdc2 and that this kinase may be involved in the mitotic reorganization of IFAP 300 by phosphorylating a mitosis-specific site. Taken together with our previous results, this study suggests that the activation of p34cdc2 coordinates the mitotic reorganization of the vimentin IF network both by severing IF-IF connections mediated by IFAP 300 and by disassembling individual IFs into protofilaments.
Induction of expression of monocyte interleukin 1 by Hageman factor (factor XII).
Authors: Toossi Z , Sedor J R , Mettler M A , Everson B , Young T , Ratnoff O D
Published: May 2006

The results reported here indicate that activated species of Hageman factor (HF, factor XII), a protein that mediates blood clotting, fibrinolysis, and activation of the complement cascade, induce elaboration of interleukin 1 (IL-1) by human monocytes. Augmentation of IL-1 production in mononuclear cell cultures was observed when HF was present along with lipopolysaccharide (LPS) but was not observed with HF alone. Furthermore, antiserum to HF abrogated the enhancement of IL-1 in cultures containing HF and LPS. Total IL-1 activity, which represents secreted and cell-associated IL-1, was enhanced in LPS-stimulated mononuclear cultures by HF. In the absence of LPS, the initial activation product of HF, HFa, which contains the serine protease enzyme activity and the surface-binding domains of the protein, induced IL-1 beta protein and mRNA. In the presence of LPS, the enzymatic moiety (HFf), which is also contained in HF and HFa, amplified IL-1 production. Induction and amplification of monocyte IL-1 by HF provides further evidence for establishing a role for HF in the acute-phase reaction and the cellular immune response.
Translocation of a folded protein across the outer membrane in Escherichia coli.
Authors: Pugsley A P
Published: May 2006

A mutation in the Escherichia coli dsbA gene (coding for a periplasmic disulfide oxidoreductase) reduces the rate of disulfide bond formation in the enzyme pullulanase and also reduces the rate at which the enzyme is secreted to the cell surface, as measured by protease accessibility. The enzyme did not become protease accessible when disulfide bond formation was completely prevented in the mutant strain by carboxymethylation. These results indicate that a disulfide bond may be required for, and certainly does not impede, the translocation of pullulanase across the outer membrane. Since it is unlikely that a disulfide bond could be formed and then reduced again in the periplasm, these results would appear to strengthen the argument that pullulanase polypeptides fold into or close to their final conformation before they are transported across the outer membrane. It is suggested that this might be a feature common to all proteins that are secreted by other Gram-negative bacteria by a pullulanase-like pathway.
Reduced expression of AP27 protein, the product of a growth factor-repressible gene, is associated with diminished adipocyte differentiation.
Authors: Wenz H M , Hinck L , Cannon P , Navre M , Ringold G M
Published: May 2006

We have recently characterized an adipocyte cDNA (clone 5) that is enhanced in expression by environmental and hormonal conditions favoring adipogenic differentiation. Moreover, certain agents including fibroblast growth factor and phorbol 12-myristate 13-acetate (but not epidermal growth factor) markedly inhibit clone 5 gene expression and prevent TA1 cell differentiation. These results led us to propose that a threshold level of the clone 5 gene product (AP27 protein) is required for triggering adipocyte differentiation. We have constructed vectors that direct the synthesis of clone 5 antisense RNA to reduce the levels of AP27 in adipogenic cell lines TA1 and 3T3-L1. We show here that when these cells express clone 5 antisense RNA, they fail to undergo morphological differentiation, whereas adipogenesis is unaffected in cells expressing antisense beta-actin or ferritin heavy-chain RNA. We further show that cells expressing clone 5 antisense RNA (but not the other antisense RNAs) are unable to induce the expression of characteristic "adipocyte-specific" mRNAs. The level of inhibition of differentiation by clone 5 antisense RNA correlates with decreased levels of AP27 protein. These results provide strong evidence that expression of AP27 is linked to adipogenic differentiation and that AP27 may be a component of an as-yet-uncharacterized signal-transduction pathway required for the triggering of adipocyte differentiation.
Regulation of glycine tRNA gene expression in the posterior silk glands of the silkworm Bombyx mori.
Authors: Taneja R , Gopalkrishnan R , Gopinathan K P
Published: May 2006

The glycine tRNA genes in silkworm Bombyx mori contain two regulatory regions upstream of the transcription start site as identified by direct transcription of 5' deletion mutants, transcription competition, gel mobility shift assays, and footprinting. A positive regulatory region is present in the immediate 5' flanking sequences of the four tRNA 1Gly clones studied. This region is essential for cell-free transcription in homologous extracts. A negative regulatory region is present farther upstream, and transcription competition experiments indicate its presence in three of the four clones examined.
Mechanism of DNase I hypersensitive site formation within the human globin locus control region.
Authors: Lowrey C H , Bodine D M , Nienhuis A W
Published: May 2006

The human beta-like globin gene locus contains embryonic, fetal, and adult globin genes that are regulated in a developmentally timed, as well as a tissue-specific, manner. The locus control region (LCR), located 5' of the globin genes, is characterized by four erythroid-specific nuclease-hypersensitive sites within native chromatin. These sites contain the active elements of the LCR. The LCR establishes an active chromatin conformation across the globin locus and enhances globin gene expression in transfected erythroleukemia cells and transgenic mice. We have used 5' DNase I hypersensitive site (HS) 4 as a model to define the minimum elements necessary for site formation. We have identified a 101-base-pair fragment within 5' HS4 that is the active site-forming element. DNase I footprint and gel-mobility shift assays have identified binding sites for transcription factors AP-1/NF-E2, Sp-1, and GATA-1 within the HS-forming element. We conclude that HS formation, the characteristic feature of the LCR in nuclear chromatin, requires interaction between erythroid-specific and ubiquitous nuclear proteins.
Studies on the initiation of simian virus 40 replication in vitro: RNA primer synthesis and its elongation.
Authors: Murakami Y , Eki T , Hurwitz J
Published: May 2006

DNA primase-dependent synthesis of oligoribonucleotides 10-15 nucleotides long was observed in the presence of ATP, UTP, GTP, and CTP by using the purified components of the simian virus 40 (SV40) DNA replication system. The DNA primase-catalyzed reaction required the SV40 large tumor antigen (T antigen), DNA polymerase alpha (pol-alpha), the three-subunit human single-stranded DNA binding protein (HSSB), and topoisomerase I. The synthesis of small RNAs was unaffected by the addition of activator 1, proliferating cell nuclear antigen, and DNA polymerase delta, proteins that can support extensive leading-strand synthesis. The RNA primers were derived predominantly from transcription of the lagging-strand template, even after prolonged incubation, indicating that the leading strand did not serve as a template. When the four dNTPs were added after oligoribonucleotide synthesis, pol-alpha extended the RNA primers hybridized to SV40 DNA. Pulse-chase experiments revealed that the small RNA chains were elongated to Okazaki-sized products. T7 DNA polymerase was also shown to rapidly extend oligoribonucleotide primers in the presence of aphidicolin or antibodies against pol-alpha, conditions under which pol-alpha was markedly inhibited. These findings suggest that interactions between T antigen, pol-alpha-primase, and HSSB position the pol-alpha-primase complex on the lagging-strand template for RNA primer synthesis.
Retrovirus insertion into herpesvirus in vitro and in vivo.
Authors: Isfort R , Jones D , Kost R , Witter R , Kung H J
Published: May 2006

Retroviruses and herpesviruses are naturally occurring pathogens of humans and animals. Coinfection of the same host with both these viruses is common. We report here that a retrovirus can integrate directly into a herpesvirus genome. Specifically, we demonstrate insertion of a nonacute retrovirus, reticuloendotheliosis virus (REV), into a herpesvirus, Marek disease virus (MDV). Both viruses are capable of inducing T lymphomas in chickens and often coexist in the same animal. REV DNA integration into MDV occurred in a recently attenuated strain of MDV and in a short-term coinfection experiment in vitro. We also provide suggestive evidence that REV has inserted into pathogenic strains of MDV in the past. Sequences homologous to the REV long terminal repeat are found in oncogenic MDV but not in nononcogenic strains. These results raise the possibility that retroviral information may be transmitted by herpesvirus and that herpesvirus expression can be modulated by retroviral elements. In addition, retrovirus may provide a useful tool to characterize herpesviral function by insertional mutagenesis.
Consequences of amino acid insertions and/or deletions in transmembrane helix C of bacteriorhodopsin.
Authors: Marti T , Otto H , Rösselet S J , Heyn M P , Khorana H G
Published: May 2006

Six bacterioopsin mutants containing either single amino acid deletions (delta A84, delta L87), insertions (delta 85A, delta 88A), or both deletions and insertions (delta A84/delta 88A, delta 85A/delta L87) within the first two turns of transmembrane helix C, starting from the extracellular side, have been prepared. The mutant apoproteins refold in phospholipid/detergent micelles and display secondary structures similar to that of the wild type. However, the mutants delta 88A and delta A84/delta 88A do not form a chromophore with retinal. The regenerated chromophore of delta 85A displays absorption maxima and retinal isomer compositions in the dark- and light-adapted states similar to those of the wild type. In delta A84, delta L87, and delta 85A/delta L87 these chromophore properties are altered, and the structures are less stable than that of the wild type, as shown by an enhanced rate of reaction with hydroxylamine in the dark, an increased pKa of the denaturation at acidic pH, and a decreased pKa of Schiff base deprotonation. Proton translocation is abolished in the delta A84 and delta 85A/delta L87 mutants, whereas in delta 85A and delta L87 the activity is reduced to about 25% of the wild-type value at pH 6. The overall properties of the delta 85A, delta 85A/delta L87, and delta L87 mutants indicate that the deletions and/or insertions result in displacement of residues Arg-82, Asp-85, or Asp-96, respectively, which participate in proton translocation. The results are compatible with a helical structure for transmembrane segment C and emphasize the flexibility of intramolecular contacts in bacteriorhodopsin.
Cardiostimulatory and antiarrhythmic activity of tubulin-binding agents.
Authors: Lampidis T J , Kolonias D , Savaraj N , Rubin R W
Published: May 2006

Rhythmic, spontaneously pulsating cardiac cells cultured from newborn rats are immediately stimulated to beat faster by addition of a number of tubulin-binding agents but not by their non-tubulin-binding analogues. The tubulin-binding agents tested include vinblastine, vincristine, navelbine, two analogs of vinblastine (S12362 and S12363), nocodazole, colchicine, and podophylotoxin. In addition to binding tubulin, all of the above agents also depolymerize microtubules. In contrast, taxol, a tubulin-binding agent that stabilizes microtubules, does not stimulate cardiac cells. Moreover, the immediate and ensuing cardiac stimulation by vinblastine at 0.05 microgram/ml is completely blocked by pre- and cotreatment with taxol at 1.0 microgram/ml. The time necessary to reverse the cardiostimulatory effect of vinblastine is significantly longer than that required for nocodazole, further implicating depolymerization of microtubules in the cardiac activity of these agents. All of the tubulin-binding agents tested (including taxol) also immediately reverse adriamycin-induced arrhythmias. By using a monoclonal antibody to alpha-tubulin, typical filamentous microtubules are visualized in cardiac muscle and cocultured non-muscle cells by immunofluorescence. When cells are treated for 2 hr with vinblastine at 0.05 microgram/ml, fluorescence is detected in cross-striated patterns in cardiac muscle cells. Overall, these data open the possibility of uncovering an additional relationship between cytoskeletal elements (other than actin and myosin) and the contractility of cardiac muscle. They also suggest an alternative mechanism for affecting cardiac cell function in vitro (namely, by tubulin-binding agents). If these agents are shown to be cardioactive in vivo, they may provide another approach to the treatment and management of cardiac arrhythmias.
Reconstitution of enzymatic activity from fragments of M1 RNA.
Authors: Guerrier-Takada C , Altman S
Published: May 2006

Certain fragments of M1 RNA, the catalytic subunit of RNase P from Escherichia coli, either have no enzymatic activity at all or have altered substrate specificity compared with that of the intact catalytic RNA. After simple mixing in vitro, many of these fragments of M1 RNA can reassociate with other fragments to form complexes that have enzymatic activity typical of wild-type M1 RNA. Furthermore, inactive M1 RNA molecules with internal deletions can be complemented in vitro by other inactive derivatives of M1 RNA that have nonoverlapping deletions. Thus, two inactive molecules of M1 RNA can interact to form an active RNA enzyme. Functional attributes can be assigned to various regions of M1 RNA when the reconstitution process is combined with assays for activity with different substrates.
Fluorescence lifetime imaging of free and protein-bound NADH.
Authors: Lakowicz J R , Szmacinski H , Nowaczyk K , Johnson M L
Published: May 2006

We introduce a methodology, fluorescence lifetime imaging (FLIM), in which the contrast depends on the fluorescence lifetime at each point in a two-dimensional image and not on the local concentration and/or intensity of the fluorophore. We used FLIM to create lifetime images of NADH when free in solution and when bound to malate dehydrogenase. This represents a challenging case for lifetime imaging because the NADH decay times are just 0.4 and 1.0 ns in the free and bound states, respectively. In the present apparatus, lifetime images are created from a series of phase-sensitive images obtained with a gain-modulated image intensifier and recorded with a charge-coupled device (CCD) camera. The intensifier gain is modulated at the light-modulation frequency or a harmonic thereof. A series of stationary phase-sensitive images each obtained with various phase shifts of the gain-modulation signal, is used to determine the phase angle or modulation of the emission at each pixel, which is in essence the lifetime image. We also describe am imaging procedure that allows specific decay times to be suppressed, allowing in this case suppression of the emission from either free or bound NADH. Since the fluorescence lifetimes of probes are known to be sensitive to numerous chemical and physical factors such as pH, oxygen, temperature, cations, polarity, and binding to macromolecules, this method allows imaging of the chemical or property of interest in macroscopic and microscopic samples. The concept of FLIM appears to have numerous potential applications in the biosciences.
Two members of a conserved family of nuclear phosphoproteins are involved in pre-mRNA splicing.
Authors: Mayeda A , Zahler A M , Krainer A R , Roth M B
Published: May 2006

Monoclonal antibody 104 recognizes a subset of amphibian nuclear granules (B-snurposomes) and active sites of RNA polymerase II transcription in vertebrates and invertebrates. Monoclonal antibody 104 reacts with a set of nuclear serine- and arginine-rich phosphoproteins (SR family) with strikingly conserved apparent molecular masses. The most abundant family members in human (SRp33) and Drosophila (SRp55) cell lines can replace one another as essential splicing factors in a human cell-free system. Each of these polypeptides can functionally replace human SF2, an essential splicing factor that also regulates 5' splice site selection of alternatively spliced pre-mRNAs in vitro. Drosophila SRp55 also functions as an alternative splicing factor in the human cell-free system. Analysis of cloned cDNAs shows that SRp55 and SF2 are highly related and reveals regions of similarity to genetically defined regulators of alternative splicing in Drosophila. These results suggest that the conserved SR family of phosphoproteins, which includes SRp55 and SF2, is involved in constitutive pre-mRNA splicing and in the specificity of alternative splice site selection.
Calcification in marine molluscs: how costly is it?
Authors: Palmer A R
Published: May 2006

Although crucial to our understanding of skeletal evolution in marine invertebrates, the cost of calcification has remained elusive for a simple reason: CaCO3 is an inorganic material. Its cost thus derives solely from the metabolic expenses of accumulating, transporting, and precipitating CaCO3 and cannot normally be separated from other metabolic costs. Traditionally, calcification cost has been ignored and total shell cost has been assumed to derive solely from skeletal organic matrix. The cost estimated here was permitted by the substantial natural variation in shell thickness in two rocky-shore gastropods (Nucella lamellosa and Nucella lapillus). In both the field and laboratory, data from three separate experiments revealed that groups of snails producing extra shell material under a particular set of experimental conditions also consumed extra food. The cost of calcification was estimated by computing the extra energy assimilated per unit extra shell produced at a common rate of tissue growth and then subtracting the cost of the organic matrix. At 1-2 J/mg of CaCO3, the calcification cost reported here is roughly 5% of that for the predominantly proteinaceous organic fraction of molluscan shells on a per-gram basis. This may explain why calcareous microstructures high in organic content have become less common evolutionarily.
The principal neutralization determinant of simian immunodeficiency virus differs from that of human immunodeficiency virus type 1.
Authors: Javaherian K , Langlois A J , Schmidt S , Kaufmann M , Cates N , Langedijk J P , Meloen R H , Desrosiers R C , Burns D P , Bolognesi D P
Published: May 2006

To identify the principal neutralization determinant (PND) of simian immunodeficiency virus (SIV), antisera were generated using recombinant gp110 [the SIV analog of the human immunodeficiency virus type 1 (HIV-1) external envelope glycoprotein, gp120], gp140, several large recombinant and proteolytic envelope fragments, and synthetic peptides of the SIVmac251 isolate. When purified under conditions that retain its native structure, gp110 bound CD4 and elicited antisera that neutralized SIVmac251 with high titer. Native gp110 also completely inhibited neutralizing antibody in sera from SIVmac251-infected macaques. In contrast, denatured gp110 and gp140, large envelope fragments, and synthetic peptides (including peptides analogous to the HIV-1 PND) elicited very low or undetectable neutralizing antibody titers and did not inhibit neutralizing antibody in infected macaque sera. Enzymatically deglycosylated gp110 efficiently absorbed neutralizing antibodies from macaque sera, showing that neutralizing antibodies primarily bind the protein backbone. A 45-kDa protease digest product, mapping to the carboxyl-terminal third of gp110, also completely absorbed neutralizing antibodies from infected macaque sera. These results show that the PND(s) of this SIV isolate depends on the native conformation and that linear peptides corresponding to the V3 loop of SIV envelope, in contrast to that of HIV-1, do not elicit neutralizing antibody. This may affect the usefulness of SIVmac for evaluating HIV-1 envelope vaccine approaches that rely on eliciting neutralizing antibody.
CD3 zeta dependence of the CD2 pathway of activation in T lymphocytes and natural killer cells.
Authors: Moingeon P , Lucich J L , McConkey D J , Letourneur F , Malissen B , Kochan J , Chang H C , Rodewald H R , Reinherz E L
Published: May 2006

In T lymphocytes, signal transduction through the CD2 adhesion molecule requires surface expression of the CD3-Ti T-cell receptor (TCR) complex. In contrast, in natural killer (NK) cells, CD2 functions in the absence of a TCR. Because the TCR on T lymphocytes and the CD16 low-affinity IgG Fc receptor (Fc gamma receptor type III) complex on NK cells share a common CD3 zeta subunit, we reasoned that CD3 zeta may be critical for CD2 signaling in T lymphocytes and NK cells. Here we show that transfection of a cDNA encoding a transmembrane form of CD16 into TCR- variants of the Jurkat T-cell line results in CD16 expression in association with endogenous CD3 zeta homodimers and restores CD2 signaling function. To test directly the role of CD3 zeta in CD2 triggering, we then transfected human CD2 into each of two murine T-T hybridomas that express TCRs containing either a full-length CD3 zeta subunit or a truncated CD3 zeta subunit incapable of transducing signals. Despite expression of equivalent surface levels of TCR, CD2-mediated signaling is seen only in the T cells containing wild-type CD3 zeta. These findings show that (i) CD16 on NK cells is functionally equivalent to the TCR on T lymphocytes for coupling CD2 to signaling pathways and (ii) CD2 signal transduction depends upon the CD3 zeta subunit of the TCR complex and, by inference, the CD3 zeta subunit of the CD16 complex.
Isolation and sequence of the granulin precursor cDNA from human bone marrow reveals tandem cysteine-rich granulin domains.
Authors: Bhandari V , Palfree R G , Bateman A
Published: May 2006

Granulins are candidate growth factors recently discovered in human and rat inflammatory leukocytes and bone marrow. Two granulin homologs, epithelin 1 and 2, occur in the rat kidney. Epithelin 1, which is probably identical to rat leukocyte granulin, exhibits proliferative and antiproliferative effects on epithelial cells in vitro. Here we show by cDNA analysis that the prepropeptide for the human granulins is a 593-residue glycoprotein, containing seven tandem repeats of the 12-cysteine granulin domain. By Northern blot analysis, gene expression was seen in myelogenous leukemic cell lines of promonocytic, promyelocytic, and proerythroid lineage, in fibroblasts and was seen very strongly in epithelial cell lines. Some epithelial cell lines respond to the mature peptide and express the gene. Among tissues examined, the kidney had the highest levels of granulin mRNA.
The 35-kDa mammalian splicing factor SC35 mediates specific interactions between U1 and U2 small nuclear ribonucleoprotein particles at the 3' splice site.
Authors: Fu X D , Maniatis T
Published: May 2006

The splicing factor SC35 is required for the first step of the splicing reaction and for the assembly of the earliest ATP-dependent complex detected by native gel electrophoresis (A complex). Here we investigate the role of SC35 in mediating specific interactions between U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) and the 5' and 3' splice sites of pre-mRNA. We show that U1 snRNP interacts specifically with both the 5' and 3' splice sites in the presence of ATP and that SC35 is required for these ATP-dependent interactions. Significantly, the SC35-dependent interaction between U1 snRNP and the 3' splice site requires U2 snRNP but not the 5' splice site. We also show that SC35 is required for the ATP-dependent interaction between U2 snRNP and the branch-point sequence. We conclude that SC35 may play an important role in mediating specific interactions between splicing components bound to the 5' and 3' splice sites.
Molecular interactions in binary solids: crystal structure of a cholesteryl ester solid solution.
Authors: Dorset D L , Pangborn W A
Published: May 2006

The x-ray crystal structure analysis of a cholesteryl ester solid solution, cholesteryl undecanoate/cholesteryl laurate in a molar ratio 0.52/0.48, is described. The unit cell is monoclinic with a = 13.005(2) A, b = 9.005(1) A, c = 31.421(3) A, and beta = 90.82(1) degrees and the space group P2(1) with Z = 4 (two molecules per asymmetric unit). Thus, the d001 spacing is almost the value predicted by Vegard's law from the values for the pure compounds. The room-temperature crystal structure is very much like that of cholesteryl laurate monolayer I packing, in the form where the esterified fatty acid chains are fully extended, with no salient sign of conformational disorder seen in this binary solid. The final R factor for 6571 observed reflections is 0.097.
A family of beta 7 integrins on human mucosal lymphocytes.
Authors: Parker C M , Cepek K L , Russell G J , Shaw S K , Posnett D N , Schwarting R , Brenner M B
Published: May 2006

The heterodimeric protein complex recognized by the human mucosal lymphocyte 1 (HML-1) monoclonal antibody is expressed on 95% of intraepithelial lymphocytes but on only 1-2% of peripheral blood lymphocytes [Cerf-Bensusson, N., Jarry, A., Brousse, N., Lisowska-Grospierre, B., Guy-Grand, D. & Griscelli, C. (1987) Eur. J. Immunol. 17, 1279-1285]. We purified the smaller HML-1 subunit (105 kDa under nonreducing conditions) from hairy-cell leukemia cells and determined the N-terminal amino acid sequence of this chain. The 17 residues determined were identical to the deduced amino acid sequence encoded by an integrin beta 7 cDNA clone [Yuan, Q., Jiang, W.-M., Krissansen, G.W. & Watson, J.D. (1990) Int. Immunol. 2, 1097-1108]. Biochemical analysis of the larger HML-1 subunit (175 kDa under nonreducing conditions) suggested that it was a distinct member of the cleaved group of integrin alpha chains, which we designated alpha E. The beta 7 chain also was associated with the integrin alpha 4 subunit, suggesting that the HML-1 antigen (alpha E beta 7) and alpha 4 beta 7 constitute a beta 7 integrin family on mucosal lymphocytes. Interestingly, regulation of the expression of the HML-1 antigen was reciprocal to that of lymphocyte function-associated molecule 1 in the presence of transforming growth factor beta 1. We suggest that these beta 7 integrins may play a specific role in mucosal localization or adhesion and that the expression of the HML-1 antigen might be regulated by transforming growth factor beta 1 produced at or near epithelial tissues.
Mutant sigma factor blocks transition between promoter binding and initiation of transcription.
Authors: Jones C H , Moran C P
Published: May 2006

The sigma subunit of bacterial RNA polymerase is required for specific binding of the enzyme to promoters. This specificity is probably directed by two regions of most sigma factors that make sequence-specific contacts at two regions of promoters, the -10 and -35 regions. We found that a single amino acid substitution in the -10 recognition region of sigma E from Bacillus subtilis trapped RNA polymerase in a stable complex with promoter DNA in which it was unable to initiate transcription. Our results are consistent with the view that promoter utilization by RNA polymerase proceeds through several intermediate steps and suggest that the -10 recognition region of sigma factors may participate in a step that follows initial promoter binding.
Differentiation of multiple domains in the herpes simplex virus 1 protease encoded by the UL26 gene.
Authors: Liu F , Roizman B
Published: May 2006

Previous studies have shown that the herpes simplex virus 1 gene UL26 encodes a 635-amino acid protease that cleaves approximately 20 amino acids from the carboxyl terminus of itself and of a 329-amino acid product of the UL26.5 gene. The results of studies with a variety of protease inhibitors showed that the UL26 protease was inhibited by serine protease inhibitors but not by inhibitors of cysteine protease, aspartic acid protease, or metalloprotease. Mutations resulting in amino acid substitutions, deletions, or insertion of stop codons in the gene or of 20-amino acid stretches into the protease have delineated the dispensable domains I and IV at the amino and carboxyl domains of the gene product. The essential carboxyl-proximal domain (III) can be separated from the essential amino-proximal domain (II) by at least 20 amino acids. The amino-proximal domain is the most conserved region among varicella-zoster virus and human cytomegalovirus homologues of UL26. Of the conserved aspartic acid, histidine, or serine amino acids in this domain, only histidine-61 and -148 could not be replaced without impairment of the proteolytic activity.
Homodimerization and constitutive activation of the erythropoietin receptor.
Authors: Watowich S S , Yoshimura A , Longmore G D , Hilton D J , Yoshimura Y , Lodish H F
Published: May 2006

The erythropoietin receptor (EPO-R) is a member of the recently described cytokine receptor superfamily. A constitutively active (hormone independent) form of the EPO-R was isolated that has a single amino acid change in the exoplasmic domain, converting arginine-129 to cysteine (R129C). Since EPO-Rs containing R129S, R129E, and R129P mutations are functionally wild type, the presence of cysteine at residue 129, and not the loss of arginine, is required for constitutive activity. Several mutant forms of the EPO-R were analyzed; all constitutively active mutants form disulfide-linked homodimers, whereas EPO-responsive or inactive forms of the receptor do not. Monomers and disulfide-linked dimers of the constitutive receptor are present on the plasma membrane and bind EPO with a single affinity. Homodimerization of the EPO-R is likely to play a role in ligand-induced signal transduction, and disulfide-linked dimerization of the constitutive receptor may mimic this step.
The interleukin 2 receptor (IL-2R): the IL-2R alpha subunit alters the function of the IL-2R beta subunit to enhance IL-2 binding and signaling by mechanisms that do not require binding of IL-2 to IL-2R alpha subunit.
Authors: Grant A J , Roessler E , Ju G , Tsudo M , Sugamura K , Waldmann T A
Published: May 2006

Interleukin 2 (IL-2)-mediated signaling through its high-affinity receptor involves a complex interrelationship between IL-2 and two IL-2-binding chains, IL-2R alpha and beta chains. Previously with the reagents available it was difficult to define functional interactions between these two IL-2R subunits involved in IL-2 binding and signal transduction. To extend our understanding of the interplay between the two binding subunits we have done studies with the monoclonal antibody HIEI, which interferes with interaction of IL-2R alpha and beta chains (IL-2R alpha and IL-2R beta, respectively). Furthermore, we used two forms of IL-2, recombinant native IL-2 and F42A, an IL-2 analog (Phe-42----Ala substitution) that binds only to IL-2R beta. Analog F42A manifested 75-100% of the bioactivity of wild-type IL-2. This observation is inconsistent with the strict hierarchical IL-2-binding affinity conversion model previously proposed by Saito and coworkers [Saito Y., Sabe, H., Suzuki, N., Kondo, S., Ogura, T., Shimizu, A. & Honjo, T. (1988) J. Exp. Med. 168, 1563-1572] that predicted an ordered sequence of events in which IL-2 must first bind to IL-2R alpha before its interaction with IL-2R beta. Previous investigations using IL-2 variants were interpreted to show that IL-2R alpha merely acts to concentrate IL-2 to the cell surface and that no other meaningful interaction occurred between IL-2R alpha and IL-2R beta. However, our data are inconsistent with this view. We draw this conclusion on the basis of our observation that antibody HIEI, which reacts with an epitope of IL-2R alpha and interferes with interaction of this chain and IL-2R beta, inhibits the IL-2-dependent proliferative effects mediated by analog F42A. Furthermore, by blocking interaction of IL-2R alpha and IL-2R beta with the antibody HIEI, a decrease in the affinity of radiolabeled analog F42A for IL-2R beta was seen. In our proposed model IL-2R alpha contributes several functions to IL-2-mediated signaling through the high-affinity IL-2R. These functions include concentration of IL-2 within the two-dimensional surface of the plasma membrane as well as alteration of the functional capacity of IL-2R beta, an effect that does not require prior binding of IL-2R to IL-2R alpha. The IL-2R alpha-mediated augmentation of IL-2R beta functions involves affinity conversion of IL-2R beta, increasing its affinity for IL-2, and may involve facilitation of Il-2-mediated signaling after binding of IL-2 to this IL-2R beta.
RNA-dependent RNA polymerase consensus sequence of the L-A double-stranded RNA virus: definition of essential domains.
Authors: Ribas J C , Wickner R B
Published: May 2006

The L-A double-stranded RNA virus of Saccharomyces cerevisiae makes a gag-pol fusion protein by a -1 ribosomal frameshift. The pol amino acid sequence includes consensus patterns typical of the RNA-dependent RNA polymerases (EC 2.7.7.48) of (+) strand and double-stranded RNA viruses of animals and plants. We have carried out "alanine-scanning mutagenesis" of the region of L-A including the two most conserved polymerase motifs, SG...T...NT..N (. = any amino acid) and GDD. By constructing and analyzing 46 different mutations in and around the RNA polymerase consensus regions, we have precisely defined the extent of domains and specific residues essential for viral replication. Assuming that this highly conserved region has a common secondary structure among different viruses, we predict a largely beta-sheet structure.
Detection of intrahepatic replication of hepatitis C virus RNA by in situ hybridization and comparison with histopathology.
Authors: Negro F , Pacchioni D , Shimizu Y , Miller R H , Bussolati G , Purcell R H , Bonino F
Published: May 2006

A nonisotopic in situ hybridization (NISH) assay was used to detect hepatitis C virus (HCV) RNA. A synthetic oligonucleotide complementary to bases 252-301 of the highly conserved 5' noncoding region of the HCV genome was end-labeled by terminal deoxynucleotidyltransferase using digoxigenin-conjugated dUTP. The hybridized oligomer was revealed by an immunohistochemical reaction after incubation with an alkaline phosphatase-conjugated anti-digoxigenin antibody and subsequent amplification with a complex of alkaline phosphatase and anti-alkaline phosphatase antibodies. The intracellular distribution of HCV RNA was monitored in the livers of two chimpanzees experimentally infected with the H strain of HCV and compared with the serum alanine aminotransferase activity, serum HCV RNA, and liver histopathology. Most cells were stained in the cytoplasm as early as 2 days after inoculation, 1 and 2 days, respectively, before the appearance of viral RNA in the serum. The time course of HCV RNA replication was correlated with increases in serum alanine aminotransferase. However, neither one paralleled the appearance of liver cell necrosis nor showed any correlation with the inflammatory response. The NISH signal was not found in liver biopsy specimens taken from these two animals before inoculation with HCV, from chimpanzees with acute hepatitis type A, B, or delta, or from two animals never experimentally infected with any hepatitis agent; moreover, it disappeared when the positive specimens were predigested with RNase and it was not observed after hybridization of positive controls with a labeled oligomer unrelated to HCV RNA. Thus, detection of liver HCV RNA by NISH is a sensitive and specific method for studying HCV replication at the cellular level. Intracellular replication of HCV did not appear to be associated with histopathologic changes in the liver, although the correlation with increases of liver enzyme activity in the serum suggested possible damage to the liver cell membrane.
Laminin-induced retinoblastoma cell differentiation: possible involvement of a 100-kDa cell-surface laminin-binding protein.
Authors: Albini A , Noonan D M , Melchiori A , Fassina G F , Percario M , Gentleman S , Toffenetti J , Chader G J
Published: May 2006

Gene and protein expression of Y-79 retinoblastoma cells growing on poly(D-lysine) is switched from a photoreceptor-like to a conventional neuron-like pathway by the basement membrane glycoprotein laminin. Unlike other cell systems where laminin influences differentiation, Y-79 cells can neither attach to nor chemotactically respond to laminin. However, laminin increases attachment to poly(D-lysine). The laminin effects therefore seem to occur via an adhesion- and chemotaxis-independent mechanism. Moreover, these tumor cells do not exhibit high-affinity laminin binding, having only a single binding site of intermediate affinity. Laminin-Sepharose affinity chromatography of Y-79 cell surface proteins labeled with 125I revealed a single major radiolabeled 100-kDa protein eluted by 20 mM EDTA, with an electrophoretic behavior different from that of integrins. No other proteins were eluted under more stringent conditions. This material, which we call LBM-100 (100-kDa laminin-binding molecule), may be a "differentiative" laminin-binding protein through which laminin influences gene expression and development independently of attachment.
A single mutation affects both N-acetylglucosaminyltransferase and glucuronosyltransferase activities in a Chinese hamster ovary cell mutant defective in heparan sulfate biosynthesis.
Authors: Lidholt K , Weinke J L , Kiser C S , Lugemwa F N , Bame K J , Cheifetz S , Massagué J , Lindahl U , Esko J D
Published: May 2006

Mutants of Chinese hamster ovary cells have been found that no longer produce heparan sulfate. Characterization of one of the mutants, pgsD-677, showed that it lacks both N-acetylglucosaminyl- and glucuronosyltransferase, enzymes required for the polymerization of heparan sulfate chains. pgsD-677 also accumulates 3- to 4-fold more chondroitin sulfate than the wild type. Cell hybrids derived from pgsD-677 and wild type regained both transferase activities and the capacity to synthesize heparan sulfate. Two segregants from one of the hybrids reexpressed the dual enzyme deficiency, the lack of heparan sulfate synthesis, and the enhanced accumulation of chondroitin sulfate, suggesting that all of the traits were genetically linked. These findings indicate that the pgsD locus may represent a gene involved in the coordinate control of glycosaminoglycan formation.
Extensive genetic diversity in the HLA class II region of Africans, with a focally predominant allele, DRB1*1304.
Authors: Hill A V , Allsopp C E , Kwiatkowski D , Taylor T E , Yates S N , Anstey N M , Wirima J J , Brewster D R , McMichael A J , Molyneux M E
Published: May 2006

Molecular HLA class II typing of greater than 1700 individuals from The Gambia in West Africa and Malawi in South-Central Africa revealed a striking diversity of HLA DRB-DQB haplotypes as defined by restriction fragment length polymorphism (RFLP); this diversity is twice as extensive as that found in northern Europeans. Despite this diversity, sequence and PCR/oligonucleotide analysis showed that the recently described variant DRB1*1304 is the commonest DRB1 allele in The Gambia. The sequence, geographical distribution, and RFLP association of this allele, together with homozygosity test results, suggest that DRB1*1304 may have arisen from DRB1*1102 and have reached its remarkably high frequency as a result of recent directional selection. The prevalence of this unusual allele has implications for trials of subunit vaccines in this area. The extensive and distinctive HLA class II region polymorphism in sub-Saharan Africans is consistent with evidence from other genetic loci implying an African origin of modern Homo sapiens.
Characterization of a growth factor that binds exclusively to the erbB-2 receptor and induces cellular responses.
Authors: Lupu R , Colomer R , Kannan B , Lippman M E
Published: May 2006

The erbB-2 oncogene encodes a 185-kDa transmembrane protein that has been suggested to be a growth factor receptor. We have previously identified and purified a 30-kDa growth factor (gp30) that is a ligand for the p185erbB-2 protein that at high concentrations induces growth inhibition of cells with erbB-2 amplification. We now report the purification and characterization of a protein from SKBr-3 human breast cancer cells with a molecular mass of 75 kDa (p75) that is a p185erbB-2 ligand. An affinity column coupled to the extracellular domain of p185erbB-2 was used for the purification. We found that p75 induced tyrosine phosphorylation of the erbB-2 oncoprotein, as determined by in vivo and in vitro phosphorylation and phosphoamino acid analysis. p75, as well as gp30, stimulated cell proliferation and colony formation of cells overexpressing erbB-2. The specificity of this effect was confirmed by showing that the antiproliferative effects of soluble erbB-2 extracellular domain were reversed by either p75 or gp30. p75 did not show binding to the epidermal growth factor receptor and had no growth effects on cells overexpressing epidermal growth factor receptor. These data show that SKBR-3 cells, which exhibit erbB-2 amplification and overexpression, secrete a growth factor that binds and activates p185erbB-2 specifically.
A gene encoding a putative tyrosine phosphatase suppresses lethality of an N-end rule-dependent mutant.
Authors: Ota I M , Varshavsky A
Published: May 2006

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. In the yeast Saccharomyces cerevisiae, mutational inactivation of the N-end rule pathway is neither lethal nor phenotypically conspicuous. We have used a "synthetic lethal" screen to isolate a mutant that requires the N-end rule pathway for viability. An extragenic suppressor of this mutation was cloned and found to encode a 750-residue protein with strong sequence similarities to protein phosphotyrosine phosphatases. This heat-inducible gene was named PTP2. Null ptp2 mutants grow slowly, are hypersensitive to heat, and are viable in either the presence or absence of the N-end rule pathway. We discuss possible connections between dephosphorylation of phosphotyrosine in proteins and the N-end rule pathway of protein degradation.
Clonal hybrids of the common laboratory fish Fundulus heteroclitus.
Authors: Dawley R M
Published: May 2006

All-female hybrids of the killifishes Fundulus heteroclitus and Fundulus diaphanus, known from two sites in Nova Scotia, Canada, are shown to reproduce clonally. Isozyme analysis of crosses between female hybrids and male F. heteroclitus reveals that their progeny are genetically identical and show no evidence of recombination or paternal inheritance. Flow cytometric measurement of DNA content shows the hybrids to be diploid, with DNA values intermediate to those of the parental species. Because they are related to F. heteroclitus, a fish used widely as a model organism in experimental biology, the clonal hybrids are potentially valuable for experimental studies requiring subjects with a constant genetic background. In addition, the discovery of unisexuality and cloning in a fish whose reproductive physiology and development are so well characterized provides a unique opportunity to examine the underlying causes of clonal reproduction in vertebrates.
A potential splicing factor is encoded by the opposite strand of the trans-spliced c-myb exon.
Authors: Vellard M , Sureau A , Soret J , Martinerie C , Perbal B
Published: May 2006

We previously established that the expression of a thymic c-myb mRNA species requires the intermolecular recombination of coding sequences expressed from transcriptional units localized on different chromosomes, in both chicken and human. We now report that a putative splicing factor (PR264), extremely well conserved in chicken and human, is encoded by the opposite strand of the c-myb trans-spliced exon. The PR264 polypeptide, which contains a typical ribonucleoprotein 80 and an arginine/serine-rich domain, is highly homologous to the Drosophila splicing regulators tra, tra-2, and su(wa) and to the human alternative splicing factor ASF/SF2. Furthermore, we show that PR264-specific mRNAs are expressed in normal hematopoietic cells of chicken and human origin and that the relative proportion of the PR264 transcripts is developmentally regulated in chicken.
First-order analysis of optical flow in monkey brain.
Authors: Orban G A , Lagae L , Verri A , Raiguel S , Xiao D , Maes H , Torre V
Published: May 2006

Optical flow is a rich source of information about the three-dimensional motion and structure of the visual environment. Little is known of how the brain derives this information. One possibility is that it analyzes first-order elementary components of optical flow, such as expansion, rotation, and shear. Using a combination of physiological recordings and modeling techniques, we investigated the contribution of the middle superior temporal area (MST), a third-order cortical area in the dorsal visual pathway that receives inputs from the medial temporal area (MT). The results show (i) that MST cells, but not MT cells, are selective for elementary flow components (EFCs) alone or their combination with translation, (ii) that MST cells selective for an EFC do not extract this component from a more complex motion pattern, and (iii) that position invariance as observed in MST is compatible with an input arrangement from MT cells matching the selectivity of MST neurons.