Cloning and sequencing of RNA-1 cDNA from cucumber mosaic virus strain O

The complete nucleotide (nt) sequence (3369 nt) of RNA 1 of cucumber mosaic virus strain O (CMV-O) was determined. One open reading frame (ORF; 993 aa) could be deduced from the nt sequence. The homologies of the ORF between CMV-O and CMV-Q or CMV-Fny were calculated to be 85% or 97%, respectively. For CMV-O and CMV-Q, the first one-third of the ORF showed a higher degree of homology (89%), as compared with the other portions (82-85%); the first 224 aa showed more than 93% homology. A comparative study of the three viruses revealed that CMV-O is more homologous to CMV-Fny (subgroup I) [corrected]) than to CMV-Q (subgroup II) [corrected].     

Defining metal ion inhibitor interactions with recombinant human H- and L-chain ferritins and site-directed variants: an isothermal titration calorimetry study

Zinc and terbium, inhibitors of iron incorporation in the ferritins, have been used for many years as probes of structure-function relationships in these proteins. Isothermal titration calorimetric and kinetic measurements of Zn(II) and Tb(III) binding and inhibition of Fe(II) oxidation were used to identify and characterize thermodynamically ( n, K, Delta H degrees, Delta S degrees, and Delta G degrees ) the functionally important binding sites for these metal ions in recombinant human H-chain, L-chain, and H-chain site-directed variant ferritins. The data reveal at least two classes of binding sites for both Zn(II) and Tb(III) in human H-chain ferritin: one strong, corresponding to binding of one metal ion in each of the eight three-fold channels, and the other weak, involving binding at the ferroxidase and nucleation sites of the protein as well as at other weak unidentified binding sites. Zn(II) and Tb(III) binding to recombinant L-chain ferritin showed similar stoichiometries for the strong binding sites within the channels, but fewer weaker binding sites when compared to the H-chain protein. The kinetics and binding data indicate that the binding of Zn(II) and Tb(III) in the three-fold channels, which is the main pathway of iron(II) entry in ferritin, blocks the access of most of the iron to the ferroxidase sites on the interior of the protein, accounting for the strong inhibition by these metal ions of the oxidative deposition of iron in ferritin.     

The immune response toward beta-adrenergic ligands and their receptors. VIII. Extensive diversity of VH and VL genes encoding anti-alprenolol antibodies

The V region genes (VH and VL) used in the immune response of BALB/c mice to alprenolol, a synthetic beta-adrenergic ligand, were examined by Southern blot and nucleotide sequence analyses. Fourteen anti-alprenolol hybridomas utilize 10 different combinations of six Vk, one V lambda, eight VH, three JK, one J lambda, and three JH genes. In addition to the combinatorial association, somatic mutations and junctional variation of assembled genes further contribute to diversity of the anti-alprenolol response. Although differing both in length and structure, the five H-chain third complementarity-determining region analyzed contain several acidic residues. Neither V gene utilization, nor H-chain third complementarity-determining-region structure can be simply correlated with affinity of the antibodies for the ligand. The anti-alprenolol V genes were compared with the corresponding sequences of unrelated antibodies. Antibody 37A4 shares a VH gene with anti-(Glu60Ala30Tyr10)n random terpolymer and anti-nitrophenyl antibodies, and a Vk gene with two anti-oxazolone antibodies. Antibodies 14C3 and 17C1 use the same germ-line VH and Vk genes as do anti-anti-idiotypic antibodies of the (Glu60Ala30Tyr10) system. These data demonstrate the genetic diversity of the antibody response to alprenolol, and illustrate the extensive flexibility of the immune system.     

Chicken immunoglobulin gamma-heavy chains: limited VH gene repertoire, combinatorial diversification by D gene segments and evolution of the heavy chain locus

cDNA clones encoding the variable and constant regions of chicken immunoglobulin (Ig) gamma-chains were obtained from spleen cDNA libraries. Southern blots of kidney DNA show that the variable region sequences of eight cDNA clones reveal the same set of bands corresponding to approximately 30 cross-hybridizing VH genes of one subgroup. Since the VH clones were randomly selected, it is likely that the bulk of chicken H-chains are encoded by a single VH subgroup. Nucleotide sequence determinations of two cDNA clones reveal VH, D, JH and the constant region. The VH segments are closely related to each other (83% homology) as expected for VH or the same subgroup. The JHs are 15 residues long and differ by one amino acid. The Ds differ markedly in sequence (20% homology) and size (10 and 20 residues). These findings strongly indicate multiple (at least two) D genes which by a combinatorial joining mechanism diversify the H-chains, a mechanism which is not operative in the chicken L-chain locus. The most notable among the chicken Igs is the so-called 7S IgG because its H-chain differs in many important aspects from any mammalian IgG. The sequence of the C gamma cDNA reported here resolves this issue. The chicken C gamma is 426 residues long with four CH domains (unlike mammalian C gamma which has three CH domains) and it shows 25% homology to the chicken C mu. The chicken C gamma is most related to the mammalian C epsilon in length, the presence of four CH domains and the distribution of cysteines in the CH1 and CH2 domains. We propose that the unique chicken C gamma is the ancestor of the mammalian C epsilon and C gamma subclasses, and discuss the evolution of the H-chain locus from that of chicken with presumably three genes (mu, gamma, alpha) to the mammalian loci with 8-10 H-chain genes.     

Analysis of a nucleic-acid-binding antibody fragment: construction and characterization of heavy-chain complementarity-determining region switch variants

The display of antibody (Ab) fragments (Fab) on the surface of filamentous bacteriophage (phage) and selection of phage that interact with a particular antigen (Ag) has enabled the isolation of Fab that bind nucleic acids. Nucleic acid (NA) binding Ab occur in vivo in connective tissue disease patients and certain inbred strains of mice and are thought to be pathogenic. Although there is ample data concerning the amino acid (aa) sequence of murine monoclonal Ab (mAb) reactive with DNA, significantly less is known about how autoAb interact with NA. The complementarity-determining regions (CDR) contained in the Fab contribute the most to Ag binding, especially through heavy (H)-chain CDR 3. We have examined the role of individual H-chain CDR of a previously isolated recombinant single-stranded DNA-binding Fab (DNA-1) in nucleic acid interaction using a combination of H-chain CDR switching and solution-binding experiments. The three H-chain CDR of DNA-1 Fab were independently switched with the H-chain CDR of a Fab (D5) with very similar sequence and framework (FR) that binds DNA poorly in order to create all possible H-chain CDR combinations. The chimeric Fab genes were bacterially expressed, and their products were purified and analyzed. Results indicated that the H-chain CDR 3 of DNA-1 Fab, in the context of the remainder of the H-chain of D5 Fab, restored binding to oligo(dT)₁₅ to 60% of DNA-1 levels, whereas H-chain CDR 1 and 3 of DNA-1 with CDR 2 of D5 Fab restored binding to 100%. A combination of H-chain CDR 2 and 3 of DNA-1 Fab with H-chain CDR 1 of D5, unexpectedly resulted in the ability of the chimeric Fab to bind RNA preferentially over DNA. These studies demonstrate the importance of both H-chain CDR 1 and 3 in DNA recognition and further suggest that the specificity of the type of NA recognized by a particular Fab can be drastically altered by exchanging CDR.     

Organization and evolution of a gene cluster for human immunoglobulin variable regions of the kappa type

An 80,000 base-pair region from the gene locus encoding the variable regions of the human immunoglobulins of the kappa type (V kappa genes) was cloned and analysed. The region comprises five V kappa sequences of subgroup I and one interspersed V kappa pseudogene of subgroup II. The six genes and pseudogenes are arranged at different distances but in the same orientation. The organization of the cluster can be explained by a series of amplification steps; the existence of a V kappa II pseudogene in a V kappa I gene cluster may have been the result of a transposition event; a final duplication step led to a second closely related copy of the cluster. From sequence data for altogether 16,000 base-pairs it appears that gene conversion-like events and subsequent selection contribute to both homogeneity and diversity of the V kappa repertoire.     

Multiple pathways for mineral core formation in mammalian apoferritin. The role of hydrogen peroxide

Human ferritins sequester and store iron as a stable FeOOH((s)) mineral core within a protein shell assembled from 24 subunits of two types, H and L. Core mineralization in recombinant H- and L-subunit homopolymer and heteropolymer ferritins and several site-directed H-subunit variants was investigated to determine the iron oxidation/hydrolysis chemistry as a function of iron flux into the protein. Stopped-flow absorption spectrometry, UV spectrometry, and electrode oximetry revealed that the mineral core forms by at least three pathways, not two as previously thought. They correspond to the ferroxidase, mineral surface, and the Fe(II) + H2O2 detoxification reactions, respectively: [see reactions]. The H-subunit catalyzed ferroxidase reaction 1 occurs at all levels of iron loading of the protein but decreases with increasing iron added (48-800 Fe(II)/protein). Reaction 2 is the dominant reaction at 800 Fe(II)/protein, whereas reaction 3 occurs largely at intermediate iron loadings of 100-500 Fe(II)/protein. Some of the H2O2 produced in reaction 1 is consumed in the detoxification reaction 3; the 2/1 Fe(II)/H2O2 stoichiometry of reaction 3 minimizes hydroxyl radical production during mineralization. Human L-chain ferritin and H-chain variants lacking functional nucleation and/or ferroxidase sites deposit their iron largely through the mineral surface reaction 2. H2O2 is shown to be an intermediate product of dioxygen reduction in L-chain as well as in H-chain and H-chain variant ferritins.     

The variability, arrangement, and rearrangement of immunoglobulin genes

The multiplicity of heavy-chain variable-region (VH) genes in mouse and human DNA has been estimated using a mouse heavy-(H) chain cDNA clone. We found about 10 hybridization components in mouse DNA and about 20 components in human DNA. Cross-hybridization studies of variable region (V) genes indicate that these components represent the numbers of genes within the VH subgroups of each of these species. The arrangement and rearrangement of the H-chain gamma subclasses have been studied in order to assess possible mechanisms of the H-chain switch. Evidence has been found for rearrangement events involving the gamma 2a and gamma 2b constant-region (CH) genes in DNA from cells making IgG2a and IgG2b respectively. In addition we found that cells making IgG2a lack detectable genes for gamma1 and gamma 2b. Both sets of observations are discussed in relation to H-chain diversity and the switch.     

A new method for the modification of fibroin heavy chain protein in the transgenic silkworm

We constructed a new plasmid vector for the production of a modified silk fibroin heavy chain protein (H-chain) in the transgenic silkworm. The plasmid (pHC-null) contained the promoter and the 3' region of a gene encoding the H-chain and the coding regions for the N-terminal domain and the C-terminal domain of the H-chain. For the model protein, we cloned a foreign gene that encoded EGFP between the N-terminal domain and the C-terminal domain in pHC-null and generated transgenic silkworms that produced a modified H-chain, HC-EGFP. Transgenic silkworms produced HC-EGFP in the posterior part of silk gland cells, secreted it into the lumen of the gland, and produced a cocoon with HC-EGFP as part of the fibroin proteins. N-terminal sequencing of HC-EGFP localized the signal sequence cleavage site to between positions A((21)) and N((22)). These results indicate that our new plasmid successfully produced the modified H-chain in a transgenic silkworm.     

Genomic typing of hepatitis C viruses present in China.

Hepatitis C virus (HCV) genomic clones were obtained from the serum of Chinese HCV carriers using a polymerase chain reaction-based approach. Consensus sequences were derived from (1) the structural region (nt 1-1543) for one carrier, (2) the hypervariable region V (nt 1156-1233) from four carriers and (3) region V3 from four carriers. Region V3, located in the nonstructural domain NS5 (nt 7066-7137), has been previously shown to be a particularly good marker for the genomic typing of HCV isolates [Inchauspe et al., Proc. Natl. Acad. Sci. USA 88 (1991) 10292-10296]. Comparison of these sequences with sequences from geographically distinct HCV isolates indicates that Chinese HCV strains are closely related to, though distinguishable from, Japanese prototype strains. One amino acid motif, GGAA, located in region V, was found to be conserved only among Chinese isolates. This may define a new subgroup among HCV isolates.     

The putative "nucleation site" in human H-chain ferritin is not required for mineralization of the iron core

It is widely believed that the putative nucleation site (Glu61, Glu64, and Glu67) in mammalian H-chain ferritin plays an important role in mineral core formation in this protein. Studies of nucleation site variant A2 (E61A/E64A/E67A) of H-chain ferritin have traditionally shown impaired iron oxidation activity and mineralization. However, recent measurements have suggested that the previously observed impairment may be due to disruption of the ferroxidase site of the protein since Glu61 is a shared ligand of the ferroxidase and nucleation sites of the protein. This study employed a new nucleation site variant A1 (E64A/E67A) which retains the ferroxidase site ligand Glu61. The data (O(2) uptake, iron binding, and conventional and stopped-flow kinetics measurements) show that variant A1 retains a completely functional ferroxidase site and has iron oxidation and mineralization properties similar to those of the wild-type human H-chain protein. Thus, in contrast to previously published literature, this study demonstrates that the putative "nucleation site" does not play an important role in iron uptake or mineralization in H-chain ferritin.     

mu-1,2-peroxo diferric complex formation in horse spleen ferritin. A mixed H/L-subunit heteropolymer

Previous kinetics studies with homopolymer ferritins (bullfrog M-chain, human H-chain and Escherichia coli bacterial ferritins) have established that a mu-1,2-peroxo diferric intermediate is formed during Fe(II) oxidation by O2 at the ferroxidase site of the protein. The present study was undertaken to determine whether such an intermediate is formed also during iron oxidation in horse spleen ferritin (HoSF), a naturally occurring heteropolymer ferritin of H and L-subunits (approximately 3.3 H-chains/HoSF), and to assess its role in the formation of the mineral core. Multi-wavelength stopped-flow spectrophotometry of the oxidative deposition of iron in HoSF demonstrated that a transient peroxo complex (lambda(max) approximately 650 nm) is produced in this protein as for other ferritins. The peroxo complex in HoSF is formed about fourfold slower than in human H-chain (HuHF) and decays more slowly (approximately threefold) as well, at an iron level of two Fe(II)/H-chain. However, as found for HuHF, a second intermediate is formed in HoSF as a decay product of the peroxo complex. Only one-third of the expected peroxo complex forms at the ferroxidase centers of HoSF when two Fe(II)/H-subunits are added to the protein, dropping to only approximately 14% when 20 Fe(II)/H-chain are added, indicating a declining role of the peroxo complex in iron deposition. In contrast to HuHF, HoSF does not enzymatically regenerate the observable peroxo complex. The kinetics of mineralization in HoSF are modeled satisfactorily by a mechanism in which the ferroxidase site rapidly produces an incipient core from a single turnover of iron, upon which subsequent Fe(II) is oxidized autocatalytically to build the Fe(O)OH(s) mineral core. This model supports a role for the L-chain in iron mineralization and helps to explain the widespread occurrence of heteropolymer ferritins in tissues of vertebrates.     

Group II twintron: an intron within an intron in a chloroplast cytochrome b-559 gene.

The psbF gene of chloroplast DNAs encodes the beta-subunit of cytochrome b-559 of the photosystem II reaction center. The psbF locus of Euglena gracilis chloroplast DNA has an unusual 1042 nt group II intron that appears to be formed from the insertion of one group II intron into structural domain V of a second group II intron. Using both direct primer extension cDNA sequencing and cDNA cloning and sequencing, we have determined that a 618 nt internal intron is first excised from the 1042 nt intron of psbF pre-mRNA, resulting in a partially spliced pre-mRNA containing a 424 nt group II intron with a spliced domain V. The 424 nt intron is then removed to yield the mature psbF mRNA. Therefore, the 1042 nt intron of psbF is a group II intron within another group II intron. We use the term 'twintron' to define this new type of genetic element. Intermediates in the splicing pathway were detected by northern hybridization. Splicing of both the internal and external introns occurs via lariat intermediates. Twintron splicing was found to proceed by a sequential pathway, the internal intron being removed prior to the excision of the external intron. A possible mechanism for twintron formation by intron transposition is discussed.     

Phenotypic differentiation of bifidobacteria of human and animal origins.

The phenotypes of 153 strains belonging or related to the genus Bifidobacterium were studied. These organisms included 38 collection strains and 115 wild strains (41 strains of human origin, 56 strains of animal origin, and 18 strains obtained from rivers or sewage). Our phenotypic analysis revealed seven main groups that were subdivided into 20 subgroups. Seven subgroups contained no type or collection strain. Among the human strains, the type strains of Bifidobacterium pseudocatenulatum and B. catenulatum fell into group I, which contained the type strains of B. adolescentis (subgroup Ib), B. dentium (subgroup Ic), and B. angulatum (ungrouped). The type strain of B. breve belonged to subgroup IIIa1, and the type strains of B. infantis and B. longum fell into subgroup IIIb1. Group VII comprised only wild strains that were isolated from human infant feces. Among the animal strains, group II consisted mainly of bifidobacteria that were isolated from pig feces and contained the type strains of B. suis (subgroup IIb), B. thermophilum (subgroup IIf), B. choerinum, and B. boum (ungrouped). Wild strains belonging to group V were isolated from pig, calf, cow, and chicken feces; this included the type strains of B. animalis (subgroup Va), B. magnum (subgroup Vb), B. pseudolongum, and B. globosum (subgroup Vc). The strains of human origin (groups I, III, and VII) were well separated from the animal strains (groups II, IV, and V). It was not surprising that the wild strains isolated from surface water or sewage were distributed in the animal groups as well as the human groups. Thus, bifidobacteria can be considered to be successful indicators of human or animal fecal pollution when they are correctly classified. The acidification patterns were not adequate to differentiate Bifidobacterium species, as determined previously by Mitsuoka (Bifidobacteria Microflora 3:11-28, 1984) and Scardovi (p. 1418-1434, in P. H. A. Sneath, N. S. Mair, M. E. Sharpe, and J. G. Holt, ed., Bergey's Manual of Systematic Bacteriology, vol. 2, 1986). However, enzymatic tests furnished new taxonomic criteria for the genus.     

Cloning, expression, and characterization of single-chain variable fragment antibody against mycotoxin deoxynivalenol in recombinant Escherichia coli

Deoxynivalenol (DON), a mycotoxin produced by several Fusarium species, is a worldwide contaminant of food and feedstuffs. The DON-specific single-chain variable fragment (scFv) antibody was produced in recombinant Escherichia coli. The variable regions of the heavy chain (V(H)) and light chain (V(L)) cloned from the hybridoma 3G7 were connected with a flexible linker using an overlap extension polymerase chain reaction. Nucleotide sequence analysis revealed that the anti-DON V(H) was a member of the V(H) III gene family IA subgroup and the V(L) gene belonged to the Vlambda gene family II subgroup. Extensive efforts to express the functional scFv antibody in E. coli have been made by using gene fusion and chaperone coexpression. Coexpression of the molecular chaperones (DnaK-DnaJ-GrpE) allowed soluble expression of the scFv. The scFv antibody fused with hexahistidine residues at the C-terminus was purified by immobilized metal affinity chromatography (IMAC). Soluble scFv antibody produced in this manner was characterized for its antigen-binding characteristics. Its biological affinity as antibody was measured by surface plasmon resonance (SPR) analysis and proved to be significant but weaker than that of the whole anti-DON mAb.     

Two unusual human immunoglobulin V kappa genes

The V kappa genes A10 and A14 which have been previously localized within the human kappa locus were analysed now. A10 hybridizes under stringent conditions only weakly or not at all to probes characteristic for the four V kappa subgroups. According to their DNA sequences and the derived amino-acid sequences A10 and A14 do not fit well into the subgroup classification. They seem to be about as closely related to the subgroup I and III genes and less related to those of subgroups II and IV. Hybridization experiments indicate that A10 and A14 belong to a small V kappa gene family. After discussing the various features of the sequences we suggest neither to assign A10 and A14 to one of the existing subgroups nor to establish a new one but to apply to them the subgroup designation N which may be changed when all V kappa genes are known and can be classified together.     

The use of zinc(II) to probe iron binding and oxidation by the ferritin (EcFtnA) of Escherichia coli

 The ferritin of Escherichia coli (EcFtnA) is similar to human H-chain ferritin (HuHF) in having 24 subunits, each containing a dinuclear site at which two iron atoms can be oxidised (the diiron centre). In EcFtnA, unlike HuHF, fluorescence quenching of Trp122, located near site A of the dinuclear centre, can be used to monitor metal binding (this tryptophan is absent from HuHF). Metal binding also perturbs the UV absorbance spectrum of Trp122 and that of Tyr24 (a conserved residue near site B of the dinuclear centre). Using UV-difference spectroscopy and fluorescence quenching it is shown that Fe(II) and Zn(II) bind at the same sites, A and B. Sequential stopped-flow studies of Fe(II) binding and oxidation also show that Zn(II) is an effective competitor of Fe(II) binding and an inhibitor of its oxidation. Received: 10 June 1998 / Accepted: 18 September 1998     

Production of an active feline interferon in the cocoon of transgenic silkworms using the fibroin H-chain expression system

We constructed the fibroin H-chain expression system to produce recombinant proteins in the cocoon of transgenic silkworms. Feline interferon (FeIFN) was used for production and to assess the quality of the product. Two types of FeIFN fusion protein, each with N- and C-terminal sequences of the fibroin H-chain, were designed to be secreted into the lumen of the posterior silk glands. The expression of the FeIFN/H-chain fusion gene was regulated by the fibroin H-chain promoter domain. The transgenic silkworms introduced these constructs with the piggyBac transposon-derived vector, which produced the normal sized cocoons containing each FeIFN/H-chain fusion protein. Although the native-protein produced by transgenic silkworms have almost no antiviral activity, the proteins after the treatment with PreScission protease to eliminate fibroin H-chain derived N- and C-terminal sequences from the products, had very high antiviral activity. This H-chain expression system, using transgenic silkworms, could be an alternative method to produce an active recombinant protein and silk-based biomaterials.