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Coating proteins: structure and cross-linking in fp-1 from the green shell mussel Perna canaliculus.

The protein family known as fp-1 provides mussel byssus with a protective outer coating and has drawn much attention for its water resistant bioadhesive properties in vitro. A new fp-l isolated from the green shell mussel Perna canaliculus (pcfp-1) reveals a composition dominated by only four amino acids: 3,4-dihydroxyphenyl-L-alanine (dopa), lysine, proline, and valine at approximately 20 mol % each. SDS-PAGE and MALDI-TOF mass spectrometry detected size variants at 48 and 52 kDa in preparations of purified Pcfp-1. The N-terminal sequence enabled construction of oligonucleotide primers for PCR and RACE-derived cDNAs from which the complete sequence of four variants was deduced. pcfp-1 deviates from all known homologues in other mussels in several notable respects: its mass is half, most of its sequence is represented by 75 tandem repeats of a tetrapeptide, i.e., PY*VK, in which Y* is dopa, prolines are not hydroxylated, and thiolate cysteines are clustered in homologous sequences at both the amino and carboxy termini. Amino acids in the repeat sequence show a striking resemblance to proline-rich cell wall proteins with tandemly repeated PPVYK pentapeptides [Hong, J. C., Nagao, R. T., and Key, J. L. (1987) J. Biol. Chem. 262, 8367-8376]. Cysteine plays a key role in cross-linking pcfp-1 by forming adducts with dopaquinone. Significant 5-S-cysteinyldopa and smaller amounts of 2-S-cysteinyldopa were detected in hydrolysates of the byssal threads of P. canaliculus. The cross-links could also be formed by oxidation of pcfp-1 in vitro using mushroom tyrosinase. Cysteinyldopa cross-links were present in trace amounts only in the byssus of other mussel species.

Adhesiveness↗

Adenovirus DNA replication in vitro: site-directed mutagenesis of the nuclear factor I binding site of the Ad2 origin.

The template requirements for efficient adenovirus DNA replication were studied in vitro in a reconstituted system with cloned DNA fragments, containing the Ad2 origin region, as templates. Replication is enhanced by nuclear factor I, a cellular protein that binds specifically to the Ad2 origin. This stimulation is shown to be strongly dependent on the concentration of the adenovirus DNA binding protein. Using synthetic oligonucleotides we have constructed plasmids with base substitutions in the nuclear factor I binding region. Footprint analysis and competition filter binding studies show that two of the three small blocks of conserved nucleotides in this region are involved in the binding of nuclear factor I. The binding affinity can be influenced by the base composition of the degenerate region just outside these two blocks. In vitro initiation and DNA chain elongation experiments with the mutants demonstrate that binding of nuclear factor I to the Ad2 origin is necessary for stimulation. However, binding alone is not always sufficient since a mutation which only slightly disturbs binding is strongly impaired in stimulation of DNA replication by nuclear factor I.

Adenoviridae↗

Positive association between expression of follicle-stimulating hormone beta and activin betaB-subunit genes in boars.

This study tested our hypothesis that inhibin/activin (I/A) betaB subunit and not follistatin (FS) gene expression relates positively to plasma FSH concentrations in the anterior pituitary gland of boars. Mature crossbred boars (n = 12) were selected for divergence in plasma FSH concentrations, and their anterior pituitary glands were evaluated for expression of the FSHbeta, I/A ssB, FS, calmodulin, and GnRH receptor (GnRH-R) genes by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) and/or RNase protection assays (RPAs). Expression of I/A ssB was greater (p < 0. 01) in the six boars with high FSH than in the six with low FSH; expression of the I/A betaB-subunit gene was positively correlated to that of the FSHbeta gene (RT-PCR: r = 0.96; p < 0.01; RPA: r = 0.68; p < 0.05). In contrast, expression of the FS (p > 0.10), GnRH-R (p > 0. 08), and calmodulin (p > 0.10) genes was similar in the two groups of boars. Additionally, expression of the FSHbeta gene was correlated positively with pituitary and plasma FSH concentrations (r = 0.69 and 0.88, respectively; p < 0.05). These results support the hypothesis that activin B is partially responsible for elevated FSH concentrations in boars. Furthermore, the expression difference of the calmodulin gene observed previously between Meishan and White Composite boars represents a breed difference unrelated to FSH.

Activins↗

Physicochemical properties of Marburg virus: evidence for three distinct virus strains and their relationship to Ebola virus.

The physicochemical and antigenic properties of three groups of Marburg (MBG) virus isolates, separated temporally and geographically, were compared to each other and to another member of the same family, Ebola (EBO) virus. Each MBG isolate contained seven virion proteins, one of which was a glycosylated surface protein. Peptide mapping of glycoproteins, nucleoproteins (NP) and viral structural protein (VP40) demonstrated extensive sequence conservation in the proteins of viruses isolated over a 13-year period, but homology was not evident in VP24. Some homology between the NPs of MBG and EBO was observed. A close antigenic relationship between MBG strains was found by radioimmunoassay but no evidence was found of antigenic cross-reactivity with EBO viruses. MBG virion proteins are produced from virus-specific monocistronic mRNA species. Five of the seven viral proteins were produced by in vitro translation of these RNAs. MBG virions contained one RNA species with an Mr of 4.2 x 10(6) and virions had a density of 1.14 g/ml in potassium tartrate. Virus isolates from different outbreaks had distinct T1 oligonucleotide maps, but had approximately 95% homology in base sequence. No two geographically distinct virus pairs were more closely related to each other than to a third virus isolate. MBG viruses are thus similar to EBO viruses in morphology and other physicochemical properties and are very similar to each other in RNA and protein composition. Each of the three geographically and temporally distinct MBG virus outbreaks appears to have been due to a genetically distinguishable, but antigenically closely related virus strain. In addition, these studies confirm the belief that MBG and EBO viruses are members of the new virus family, the Filoviridae.

Animals↗

Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella.

Horizontal gene transfer plays a major role in microbial evolution. However, newly acquired sequences can decrease fitness unless integrated into preexisting regulatory networks. We found that the histone-like nucleoid structuring protein (H-NS) selectively silences horizontally acquired genes by targeting sequences with GC content lower than the resident genome. Mutations in hns are lethal in Salmonella unless accompanied by compensatory mutations in other regulatory loci. Thus, H-NS provides a previously unrecognized mechanism of bacterial defense against foreign DNA, enabling the acquisition of DNA from exogenous sources while avoiding detrimental consequences from unregulated expression of newly acquired genes. Characteristic GC/AT ratios of bacterial genomes may facilitate discrimination between a cell's own DNA and foreign DNA.

Bacterial Proteins↗

Biochemical characterization of a novel autocrine transferrin-like growth factor in acute myeloblastic leukemia.

Serum-free conditioned media (CM) of acute myelogenous leukemia cell lines induce growth stimulation of other leukemic cell lines. A transferrin (Tf)-like iron binding kD 50 protein was found to be the main growth factor of these CM's. Purification and further characterization of this protein was performed by chromatographic methods, SDS-PAGE, peptide mapping and amino acid analysis. In addition m-RNA of leukemic cell lines was analysed by Northern blot analysis with oligonucleotide probes specific for human serum Tf and melanotransferrin (p97) respectively. No hybridization signals for these probes have been detected. Biochemical results show significant differences between human serum Tf and kD 50 growth factor with respect to retention time on reversed phase FPLC, pattern of digestion peptides in SDS-PAGE and amino acid composition, which suggests, that this protein is an additional tumor associated member of the transferrin superfamily.

Amino Acids↗

Predicting regional mutability in antibody V genes based solely on di- and trinucleotide sequence composition.

Somatic mutations are not distributed randomly throughout Ab V region genes. A sequence-specific target bias is revealed by a defined hierarchy of mutability among di- and trinucleotide sequences located within Ig intronic DNA. Here we report that the di- and trinucleotide mutability preference pattern is shared by mouse intronic JH and Jkappa clusters and by human VH genes, suggesting that a common mutation mechanism exists for all Ig V genes of both species. Using di- and trinucleotide target preferences, we performed a comprehensive analysis of human and murine germline V genes to predict regional mutabilities. Heavy chain genes of both species exhibit indistinguishable patterns in which complementarity-determining region 1 (CDR1), CDR2, and framework region 3 (FR3) are predicted to be more mutable than FR1 and FR2. This prediction is borne out by empirical mutation data from nonproductively rearranged human VH genes. Analysis of light chain genes in both species also revealed a common, but unexpected, pattern in which FR2 is predicted to be highly mutable. While our analyses of nonfunctional Ig genes accurately predicts regional mutation preferences in VH genes, observed relative mutability differences between regions are more extreme than expected. This cannot be readily accounted for by nascent mRNA secondary structure or by a supplemental gene conversion mechanism that might favor nucleotide replacements in CDR. Collectively, our data support the concept of a common mutation mechanism for heavy and light chain genes of mice and humans with regional bias that is qualitatively, but not quantitatively, accounted for by short nucleotide sequence composition.

Animals↗

Heterochromatin and chromosome evolution: a FISH probe of Cebus apella paraguayanus (Primate: Platyrrhini) developed by chromosome microdissection.

Neotropical Primate karyotypes are highly variable, particularly in the heterochromatic regions, not only regarding the amount of heterochromatin, but also the composition. G and C banding and FISH techniques provide useful information to characterize interspecific relationships. We used chromosome microdissection to develop a FISH probe of the chromosome 11 heterochromatic block (11qHe+) of Cebus apella paraguayanus (CAPp). Fragments of the 11qHe+ microdissected from fibroblast cell culture were collected in a PCR tube, amplified by degenerate oligonucleotide primer-PCR and subsequently labeled. The specificity of the FISH probe was confirmed in metaphases of some Ceboidea species. Signals were located in the He+ of chromosomes 4, 11, 12, 13, and 19 of CAPp and in the He+ of chromosomes 4, 12 and 13 of C. a. nigritus (CAPn); no signals were observed when other Ceboidea species were analyzed. We propose that the heterochromatin observed in CAPp and CAPn is specific for these species. We consider this C. apella heterochromatin identity as a possible key for the interpretation of chromosomal evolution in these Ceboidea.

Animals↗

Effect of length, supercoiling, and pH on intramolecular triplex formation. Multiple conformers at pur.pyr mirror repeats.

The conformations adopted by five oligopurine.oligopyrimidine (pur.pyr) inserts of various lengths and sequence repeats in recombinant plasmids were evaluated as a function of pH and negative super-helicaldensity. Patterns of chemical reactivity (OsO4 and diethylpyrocarbonate) indicate that long (greater than 36 base pairs) pur.pyr segments can adopt intramolecular triplexes and that increasing the length of the pur.pyr tract reduces the dependence on low pH for structure formation, such that (GA)37 adopts an intramolecular triplex under moderate levels of negative superhelical stress (-sigma = 0.049) at neutral pH. This demonstrates that long pur.pyr segments, which are abundant in eukaryotic genomes, have the potential to adopt triplexes in vivo. Two-dimensional gel electrophoresis of the plasmids combined with chemical probing indicates that for longer sequences, multiple conformers of the intramolecular triplex exist at low pH. These conformers result from nucleation at various positions on the polypurine stretch, giving rise to different extents of relaxation at the same linking number. In addition, the metal ions Co2+, Mn2+, and Mg2+ have profound effects on the pattern of chemical reactivity displayed by long pur.pyr segments at both neutral and low pH, indicating that quite different structures may form in the presence of divalent metal ions. Thus, the types and extent of unusual structures adopted by long pur.pyr segments are complex and heterogeneous, and are dependent on pH, supercoiling, and the presence of divalent cations.

Base Composition↗

Rapid identification of Vibrio vulnificus on nonselective media with an alkaline phosphatase-labeled oligonucleotide probe.

An oligonucleotide DNA probe (VVAP) was constructed from a portion of the Vibrio vulnificus cytolysin gene (hylA) sequence and labeled with alkaline phosphatase covalently linked to the DNA. Control and environmental isolates probed with VVAP showed an exact correlation with results obtained with a plasmid DNA probe (derived from pCVD702) previously described as having 100% specificity and sensitivity for this organism. Identification of V. vulnificus strains was confirmed independently by analysis of the cellular fatty acid composition and by API 20E. Naturally occurring V. vulnificus bacteria were detected without enrichment or selective media by VVAP in unseeded oyster homogenates and seawater collected from a single site in Chesapeake Bay during June at concentrations of 6 x 10(2) and 2 x 10(1) bacteria per ml, respectively. V. vulnificus bacteria were also enumerated by VVAP in oysters seeded with known concentrations of bacteria and plated on nonselective medium. The VVAP method provides a rapid, accurate means of identifying and enumerating V. vulnificus in seawater and oysters without the use of selective media or additional biochemical tests.

Alkaline Phosphatase↗

Physicochemical characterization of protamine-phosphorothioate nanoparticles.

Protamine-oligonucleotide nanoparticles represent effective colloidal drug carriers for antisense phosphorothioate oligonucleotides (PTO). This study describes improvements in particle preparation and the physicochemical properties of the complexes prepared. The influence of component concentrations, length of the PTO chain and the PTO/protamine weight ratio on particle formation and size, shape and surface charge of the particles were studied in detail. Nanoparticles with diameters of 90-200nm were obtained, using protamine free base (PFB) and phosphorothioate in water. The chemical composition of the nanoparticles was analysed. More than 90% of the PTO could be assembled in the particle matrix using a > or = 1:2 ratio (w/w) of PTO and PFB. About 53-68% of the PFB was incorporated in the particle matrix. The complexes had a zetapotential of -19 up to +32 mV, depending on the PTO/PFB ratio. The kinetics of the assembly of this binary system were observed by dynamic light scattering (DLS) measurements and by sedimentation velocity analysis in the analytical ultracentrifuge (AUC). In addition, scanning electron microscopy (SEM) and atomic force microscopy (AFM) were applied to verify the results of DLS and the ultracentrifuge measurements. According to sedimentation velocity analysis, the particles were only moderately stable in water and unstable in salt solutions. However, the colloidal solution in water could be stabilized by polyethylenglycol 20000 (PEG), which also led to an increase of stability in cell medium.

Chemical Phenomena↗

Characteristics of a swine recombinant influenza virus isolated in 1980: recombination between swine and the earliest Hong Kong (H3N2) viruses.

A recombinant (H1N2, formerly Hsw1N2), A/swine/Ehime/1/80 was found to possess antigenic biological and genomic characteristics different from those of a previous A/swine/Kanagawa/2/78 (H1N2) strain. Five monoclonal antibodies to A/NJ/8/76 differentiated the haemagglutinin molecules of the former virus from the latter, showing that these viruses differed at two-antigenic determinants at least. Immuno-double diffusion tests with antisera to the isolated neuraminidase and neuraminidase-inhibition tests with monoclonal antibodies to different H2N2 and H3N2 viruses revealed that A/swine/Ehime/1/80 strain contained a neuraminidase subunit very similar to that of late human Asian (H2N2) and the earliest Hong Kong (H3N2) viruses. RNA analysis by oligonucleotide mapping suggested that A/swine/Ehime/1/80 may be a recombinant between A/swine/Shizuoka/1/78-like and A/Aichi/2/68 (H3N2)-like viruses. To determine further the gene constellation of this recombinant virus, DNA-RNA hybridizations were performed using DNA segments complementary for swine (H1N1) virus RNA and the entire RNA of three viruses. The molecular hybridization could define the genomic composition of the recombinant, indicating that only the neuraminidase gene of this virus is derived from the earliest Hong Kong (H3N2)-like virus and remaining seven genes are derived from swine (H1N1) virus.

Animals↗

A molecular dissection of the interaction between the transcription factor Gata-1 zinc finger and DNA.

The production of circulating blood cells from bone marrow stem cells during hematopoiesis is accompanied by overall changes in gene expression which cause production of required functional proteins, such as hemoglobin in erythroid cells, as well as control of cell growth, preventing apoptosis of differentiating cells. Hematopoietic gene regulation is controlled by several specific transcription factors, including the factor Gata-1, which is required for erythrocyte maturation. Based on contacts observed in the NMR structure of the cGata-1 binding domain in complex with DNA, the protein's key DNA interface is interesting in being quite hydrophobic in nature, due to the presence of three leucine side chains protruding toward the DNA. Given the T-rich composition of the GATA DNA binding site, it is possible that thymine's unique 5-methyl group may mediate some of these hydrophobic contacts to increase the stability of binding. The hypothesis that thymine methyl groups are important to the free energy of binding between Gata and DNA is tested by measuring binding of an oligonucleotide substrate in which individual thymine bases are substituted with uracil. To test for any important base-pair specific interactions which may be hydrogen-bonded in character, we have also assayed Gata binding to oligonucleotides with base analogs which cannot make hydrogen bonds. We report that out of the binding site's five thymine methyl groups, only one appeared to make a notable contribution to binding affinity, with removal causing a loss of less than 1kcal/mol of binding free energy. On the other hand, perturbing the potential hydrogen-bonding surface of the DNAs major groove was found to cause a larger decrease in binding affinity than removal of any of the thymine methyl groups, with a loss of 2-3kcal/mol of binding free energy.

Amino Acid Sequence↗

Single-base mismatch detection based on charge transduction through DNA.

High-throughput DNA sensors capable of detecting single-base mismatches are required for the routine screening of genetic mutations and disease. A new strategy for the electrochemical detection of single-base mismatches in DNA has been developed based upon charge transport through DNA films. Double-helical DNA films on gold surfaces have been prepared and used to detect DNA mismatches electrochemically. The signals obtained from redox-active intercalators bound to DNA-modified gold surfaces display a marked sensitivity to the presence of base mismatches within the immobilized duplexes. Differential mismatch detection was accomplished irrespective of DNA sequence composition and mismatch identity. Single-base changes in sequences hybridized at the electrode surface are also detected accurately. Coupling the redox reactions of intercalated species to electrocatalytic processes in solution considerably increases the sensitivity of this assay. Reporting on the electronic structure of DNA, as opposed to the hybridization energetics of single-stranded oligonucleotides, electrochemical sensors based on charge transport may offer fundamental advantages in both scope and sensitivity.

Base Pair Mismatch↗

A PCR-derived library of random point mutations within the V3 region of simian immunodeficiency virus.

Oligonucleotide primers corresponding to variable region 3 (V3) of simian immunodeficiency virus (SIV) were randomly mutagenized during synthesis by doping each of the four nucleoside phosphoramidites with a small amount of the other three. PCR was then used to incorporate the altered sequences into larger, clonable DNA fragments by spliced overlap extension (SOE). With the composition of the phosphoramidites used, 53 of the 100 clones analyzed were unique, having one or more point mutation within the 84-bp target sequence. These 53 unique clones contained an average of 2.1 nucleotide substitutions and 1.5 amino acid substitutions per clone within the target V3 sequence. Of the internal 25 amino acid positions within the V3 domain, 23 were changed at least once. This method should be generally useful for the construction of libraries of random point mutations within a defined target DNA sequence.

Amino Acid Sequence↗

[Halophilic archaea flagella: biochemical and genetic analysis].

The protein compositions of archaebacteria (Halobacterium salinarium, Halobacterium volcanii, Halobacterium saccharovorum and Natronobacterium pharaonis 12) flagella have been studied. It was found that flagella of these archaebacterial species are made up of flagellins. The flagellins of H. salinarium, H. volcanii and H. saccharovorum are glycosylated. Based on the known primary sequences of Halobacterium halobium R1M1 flagellin genes, oligonucleotides to the 5'- and 3'-ends of locus A containing two out of five such genes have been synthesized. The amplified by primers fragment of chromosomal DNA coding for H. halobium flagellins A1 and A2 was used as a probe for detecting homologous sites in archaebacterial DNA. Southern blotting hybridization revealed that the DNA of all archaebacterial species tested in this study contains sequences that are homologous to genes flg A1 and flg A2 of H. halobium.

Archaea↗

Human non-histone chromosomal protein HMG-17: identification, characterization, chromosome localization and RFLPs of a functional gene from the large multigene family.

The multigene family of chromosomal protein HMG-17 is the largest known human retropseudogene family. A functional gene was identified and isolated by screening cDNA-selected genomic clones with a set of 5 oligonucleotides whose sequence corresponded to regions in which the sequence of the retropseudogenes differed from that of the cDNA and which did not span previously identified exon/intron junctions. A 7195 bp genomic fragment containing 6 exons, ranging in size from 30 to 817 bp, two of which encode the entire DNA binding domain of the protein, was sequenced. The gene has features which are typical to "housekeeping" genes and is characterized by a very high content of G + C residues in a 1.4 kb fragment starting 500 bp from the cap site and by an "HTF" island in the 5' region. Transcriptional regulatory signals, exon/intraon boundaries and features characteristic of "housekeeping" genes are evolutionary conserved between the human and chicken genes. The HMG-17 gene was localized to human chromosome 1p12-34. RFLP's useful for further mapping were detected. The experimental evidence presented leads to the assumption that the gene characterized is the only functional human HMG-17 gene.

Amino Acid Sequence↗

Oligonucleotide directed triple helix formation.

Oligonucleotide directed triple helix formation allows the sequence-specific recognition of the major groove of double-helical DNA. Recently synthesized base analogs and backbones, such as N3'-->P5' phosphoramidates, allow stable triplexes to be formed under physiological conditions. However, it remains a challenge to design new oligomers that would extend the range of recognition sequences (which are still limited to oligopurine-rich tracts). Oligonucleotide directed triple helix formation could be used to control biological processes such as transcription and replication. Three-stranded structures formed during recombination processes have been further characterized.

Base Composition↗