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PubMed1985

Mapping of the C3d receptor (CR2)-binding site and a neoantigenic site in the C3d domain of the third component of complement.

The C3d domain of C3 contains the site that binds to the C3d receptor (CR2) which is expressed on B lymphocytes. It also contains a neoantigenic determinant that is recognized by monoclonal antibody (mAb) 130 and is expressed when C3b is cleaved to iC3b and subsequently to C3dg or C3d. mAb 130 inhibits the binding of C3d to CR2. In this study, the locations of the CR2-binding site and of the neoantigen recognized by mAb 130 within the C3d domain were investigated. Treatment of human C3d with CNBr generated two major fragments with Mrs of 12,500 and 8600. Binding studies showed that only the Mr 8600 fragment was capable of binding to both CR2 and mAb 130. Amino-terminal sequence analysis of the Mr 8600 fragment and comparison with the amino acid sequence derived from human C3 cDNA [de Bruijn, M. H. L. & Fey, G. H. (1985) Proc. Natl. Acad. Sci. USA 82, 708-712] placed it between residues 1199 and 1274 of the C3 sequence. Several peptides were synthesized according to the derived C3 sequence of amino acid residues 1209-1236. Based on their differential binding to CR2 and mAb 130, we localized the CR2-binding site and mAb 130 neoantigenic site, respectively, to residues 1227-1232 and 1217-1232 of the C3 sequence.

Amino Acid Sequence↗
PubMed2003

Characterization of genotype II Rubella virus strains.

Two genotypes of Rubella virus have been described that differ by 8-9% at the nucleotide level in the E1 glycoprotein gene. Of these, genotype II (RGII) was only recently reported and in this study two RGII viruses, the BRDII vaccine strain and BR1 wild type strain, were characterized. Monoclonal antibodies against each of the virion proteins (capsid [C], glycoproteins E1 and E2) and polyclonal anti-rubella virus sera reacted similarly with purified virions from the RGII and reference RGI strains on Western gels, with the exception of one anti-E2 Mab, and thus the two genotypes are closely related antigenically. The genomic sequences of two genotype II (RGII) rubella virus strains were determined and compared with the six previously reported RGI sequences. The genomes of these viruses all contained 9762 nts and the lengths of the three untranslated regions (UTRs) and two open reading frames (ORF's) were identical. The overall difference between the RGI and RGII sequences at the nt level was approximately 8% and this difference was maintained across most of the genome. At the amino acid level, the RGI and RGII sequences differed overall by approximately 4%, however this difference was not uniform across the ORF's as the N-terminal third of P150 and the entirety of P90, both replicase proteins, were more conserved (<1% difference) while the C-terminal two thirds of P150 exhibited greater variation ( approximately 8% difference), including a hypervariable region between residues 771-801 within which divergence as great as 20-30% was detected. The parent wt virus of the BRDII vaccine was not available and its sequence was compared with the BR1 sequence to identify potential attenuating mutations. The BRDII and BR1 sequences varied at 252 residues (2.59%), including twelve in the UTRs and thirty coding differences in the ORF's. None of these differences in the BRDII sequence was vaccine-specific when compared with RGI wt and vaccine sequences and, therefore, there appeared to be no common pathway in the generation of live, attenuated rubella vaccines.

3' Untranslated Regions↗
PubMed2006

Assembly of the Tc1 and mariner transposition initiation complexes depends on the origins of their transposase DNA binding domains.

In this review, we focus on the assembly of DNA/protein complexes that trigger transposition in eukaryotic members of the IS630-Tc1-mariner (ITm) super-family, the Tc1- and mariner-like elements (TLEs and MLEs). Elements belonging to this super-family encode transposases with DNA binding domains of different origins, and recent data indicate that the chimerization of functional domains has been an important evolutionary aspect in the generation of new transposons within the ITm super-family. These data also reveal that the inverted terminal repeats (ITRs) at the ends of transposons contain three kinds of motif within their sequences. The first two are well known and correspond to the cleavage site on the outer ITR extremities, and the transposase DNA binding site. The organization of ITRs and of the transposase DNA binding domains implies that differing pathways are used by MLEs and TLEs to regulate transposition initiation. These differences imply that the ways ITRs are recognized also differ leading to the formation of differently organized synaptic complexes. The third kind of motif is the transposition enhancers, which have been found in almost all the functional MLEs and TLEs analyzed to date. Finally, in vitro and in vivo assays of various elements all suggest that the transposition initiation complex is not formed randomly, but involves a mechanism of oriented transposon scanning.

Amino Acid Sequence↗
PubMed2004

A score matrix to reveal the hidden links in glycans.

MOTIVATION: Glycans are the third major class of biomolecules following DNA and proteins. They are extremely vital for the functioning of multicellular organisms. However, comparing the fast development of sequence analysis techniques, informatics work on glycans have a long way to go. Alignment algorithms for glycan tree structures are one of the foremost concerns. In addition, the statistical analysis of these algorithms in terms of biological significance needs to be addressed. RESULTS: We developed a tree-structure alignment algorithm for glycans and performed a statistical analysis of these alignment scores such that biologically interesting features could be captured into a score matrix for glycans. We generated our score matrix in a manner similar to BLOSUM, but with slight variations to accomodate our glycan data, including the incorporation of linkage information. We verified the effectiveness of our new glycan score matrix by illustrating how well the resulting score matrix entries correspond with biological knowledge. Future work for even better improvements with the use of a variety of score matrices for different subclasses of glycans due to their complexity is also discussed. CONTACT: mami@kuicr.kyoto-u.ac.jp SUPPLEMENTARY INFORMATION: The glycan score matrix can be downloaded from http://kanehisa.kuicr.kyoto-u.ac.jp/Paper/kcam/glycanMatrix0.1.txt.

Algorithms↗
PubMed1989

Length heterogeneity in rat salivary gland alpha 2 mu globulin mRNAs: multiple splice-acceptors and polyadenylation sites.

Rat alpha 2 mu globulins are coded for by a family of about 25 structurally related genes, some of which are expressed in the male adult liver while the other subset seems to be active in several excretory organs, including salivary and lacrymal glands. To estimate the number and specificity of genes expressed in the salivary glands, we determined nucleotide sequences of 30 cDNA clones. At least two alpha 2 mu globulin genes are active and two thirds of mRNAs were shown to code for the peptide two amino acids shorter than the others. Unexpected observation was the intense length polymorphism in the 3' non-coding 6th intron-7th exon regions presumably caused by alternative splice-acceptor selection. At least six acceptor sites were utilized and the longest type retained the entire 6th intronic sequence resulting in a formation of unusually longer product. A stable mRNA molecule of this type was demonstrated in salivary glands by Northern blotting probed with the 6th intron-specific fragment. Together with three independent polyadenylation sites, the rat salivary glands generate a diverse set of alpha 2 mu globulin mRNAs.

Alpha-Globulins↗
PubMed1994

Differentiation of Salmonella serovar infantis isolates from human and animal sources by fingerprinting IS200 and 16S rrn loci.

We genotyped Salmonella serovar infantis (referred to as S. infantis), which is the most widespread serovar among animals and the third most common cause of human salmonellosis in Finland. Molecular fingerprinting of the 16S rrn locus and the Salmonella-specific insertion sequence IS200 was used to type the 131 isolates originating from the main sources of S. infantis infection. The number of IS200 elements in S. infantis varied from zero to seven; three or more copies were present in 97% of the isolates, and 71% had four copies. There were four conserved chromosomal positions of IS200, which allowed us to group the isolates into three major clonal groups. We defined 11 unique IS200 profiles and five different ribotypes which, in combination, generated 15 genotypes highly restricted to the infection sources: 8 genotypes were typical of isolates from broiler chickens and cattle and seven genotypes were typical of isolates from humans. The eight genotypes of isolates from chickens represented two clonal groups which were differentially associated with chicken-producing companies. The typing scheme allows efficient discrimination between isolates from various infection sources and within sources and, therefore, provides a unique molecular tool for use in the study of the epidemiology of S. infantis infection.

Animals↗
PubMedDate not supplied

Periodicities of dinucleotide self-information values in phi X174 DNA.

The natural DNA sequence of bacteriophage, phi X174, when analyzed as a "text" of dinucleotides, is shown to display an easily detectable degree of non-randomness by the distribution of values of dinucleotide self-information along the sequence. Self-information corresponding to occurrences of dinucleotides separated by a single nucleotide is found to be somewhat higher than the values which precede or follow it for every third nucleotide position along the sequence. Consequently autocorrelation coefficients of these values display a strong periodicity and harmonic analysis of the values shows a spike at a value of 3. Self-information autocorrelation periodicity is used as a test of the effect of randomizing portions of the sequence. Any one or two of the three nucleotides in each triplet of the sequence can be chosen at random without losing dinucleotide self-information periodicity except when both the 1st and 3rd nucleotide of all of the triplets in the major phi X174 protein reading frame are randomized. Periodicity is also lost when sequences are generated by randomizing triplets. Autocorrelation and harmonic analysis also indicate other less marked periodic features of dinucleotide self-information values of the nature sequence; non-random features are suggested at periods of 12, 20 and 24 nucleotides.

Bacteriophage phi X 174↗
PubMed2000

[Effects of bodily movement and verbal information on memory for action events].

The purpose of this study was to examine effects of bodily movement and verbal information on memory representation of an action. Whether the subject actually performed the action (SPTs) or he/she saw the experimenter do (EPTs) was bodily movement factor. Whether a verbal description of the sequence was given or not was verbal information factor. The two factors formed four groups in Experiment 1, and 56 subjects participated, using two kinds of memory material as a third factor: instruments and bodily movement. Supplemental analyses were the purpose of Experiment 2, in which 112 subjects in eight groups participated, examining verbal or motor recall and recognition. Results of the two experiments suggested that bodily movement facilitated integration of verbal and motor-action components when verbal information was also present. In addition, it was suggested that bodily movement helped form 'motor imagery' as memory representation, which was utilized at generation stage of memory retrieval and verifying stage of motor recognition. With these results, the relationship between processing of verbal component and that of motor-action component was discussed.

Adult↗
PubMed1989

The c-erbA alpha-encoded thyroid hormone receptor is phosphorylated in its amino terminal domain by casein kinase II.

The c-erbA alpha progenitor of the v-erbA oncogene of avian erythroblastosis virus (AEV) encodes a nuclear receptor for the thyroid hormone triiodothyronine (T3) which acts as a ligand-dependent transcription factor. As previously reported (Goldberg et al., EMBO J., 7, 2425-2433), the 46 kd chicken c-erbA alpha-encoded T3 receptor (ck-ErbA alpha) is phosphorylated at two major sites. Only one of these sites (Ser28/Ser29) is retained in the v-erbA-encoded P75gag-v-erbA protein. We report here the identification of the second phosphorylation site of ck-ErbA alpha as a single serine residue localized at position 12. We propose that casein kinase II, a protein kinase distributed in the cytosolic and nuclear compartments of a number of different tissues, is responsible for serine 12 phosphorylation on the following grounds. First, serine 12 is part of a sequence containing multiple acidic amino-acids, a feature common to all sites phosphorylated by casein kinase II in physiological substrates. Second, ck-ErbA alpha was found to be phosphorylated by purified casein kinase II in vitro at the same site, as defined by two-dimensional mapping experiments, as that observed in vivo. Third, conversion of serine 12 into an unphosphorylatable alanine residue by site directed mutagenesis abolishes the phosphorylation of ck-ErbA alpha by casein kinase II in vitro. Phosphorylation of serine 12 is likely to play a role in the modulation of ErbA alpha function since both serine 12 and the casein kinase II phosphorylation sequence motif are phylogenetically conserved in all known members of the c-erbA alpha gene family encoding T3 binding proteins. The codon specifying serine 12 in ck-ErbA alpha being precisely the point where recombination between gag and ck-c-erbA alpha occurred to generate v-erbA, our results furthermore suggest that deletion of serine 12 could contribute to the oncogenic activation of v-erbA.

Amino Acid Sequence↗
PubMed1996

Binding and incision activities of UvrABC excinuclease on slipped DNA intermediates that generate frameshift mutations.

Previous in vivo studies involving sequence 5'-CCCG1G2G3-3' (SmaI site) have demonstrated that adducts of N-2-acetylaminofluorene (AAF) to any of the three guanine residues of the SmaI sequence induce, with different efficiencies, two classes of -1 frameshift events, namely -G and -C mutations, referred to as targeted and semitargeted mutations, respectively. It has been proposed that both events occur during replication as a consequence of slippage events involving slipped mutagenic intermediates (SMIs). In order to evaluate the potential role of the UvrABC excinuclease in frameshift mutagenesis, we have studied the interaction of this enzyme with DNA molecules mimicking SMIs in vitro. In all of our constructions, when present, the AAF adduct was located on the third guanine residue of the SmaI site (5'-CCCG1G2G3-3'). This strand was referred to as the top strand, the complementary strand being the bottom strand. Double-stranded heteroduplexes mimicking the targeted and semitargeted SMIs contained a deletion of a C and a G within the SmaI sequence in the bottom strand and were designated deltaC/3 and deltaG/3 when modified with the AAF on the third guanine residue in the top strand or deltaC/O and deltaG/O when unmodified. The modified homoduplex was designated SmaI/3. deltaC/O and deltaG/O were weakly recognized by UvrA2B, but not incised. All three AAF-modified substrates were recognized with similar efficiency and much more efficiently than unmodified heteroduplexes. With AAF-monomodified substrates, dissociation of UvrA2 from the UvrA2B-DNA complex occurred more readily in heteroduplexes than in the homoduplex. SmaI/3 and deltaC/3 were incised with equal efficiency, while deltaG/3 was less incised. The position of the AAF lesion dictated the position of the incised phosphodiester bonds, suggesting that the presence of a bulge can modulate the yield but not the incision pattern of AAF-modified substrates. The finding that UvrABC excinuclease acts on substrates that mimic SMIs suggests that the nucleotide excision repair pathway may help in fixing frameshift mutations before the following round of replication.

2-Acetylaminofluorene↗
PubMed1996

Mapping the lipid-exposed surfaces of membrane proteins.

Phospholamban forms a stable complex of five long transmembrane helices. We show that the relative rotational orientation of the helices in the pentameric complex can be distinguished by S-H to S-D exchange of cysteine sulphydryl groups located in the transmembrane segment of the protein and exposed to the lipid environment. Of the three cysteine residues in phospholamban, two residues (Cys 36 and Cys 46) are oriented towards the helix interface and protected from exchange, while the third cysteine (Cys 41) is oriented towards the lipid interface and undergoes exchange with water diffused into the bilayer. Distinguishing the external and internal faces of a membrane protein by sulphydryl exchange provides a general approach for determining the three-dimensional fold of membrane proteins and enhances model building efforts to generate high-resolution structures.

Adenosine Triphosphatases↗
PubMed2003

Hookworm aspartic protease, Na-APR-2, cleaves human hemoglobin and serum proteins in a host-specific fashion.

Hookworms are voracious blood-feeders. The cloning and functional expression of an aspartic protease, Na-APR-2, from the human hookworm Necator americanus are described here. Na-APR-2 is more similar to a family of nematode-specific, aspartic proteases than it is to cathepsin D or pepsin, and the term "nemepsins" for members of this family of nematode-specific hydrolases is proposed. Na-apr-2 mRNA was detected in blood-feeding, developmental stages only of N. americanus, and the protease was expressed in the intestinal lumen, amphids, and excretory glands. Recombinant Na-APR-2 cleaved human hemoglobin (Hb) and serum proteins almost twice as efficiently as the orthologous substrates from the nonpermissive dog host. Moreover, only 25% of the Na-APR-2 cleavage sites within human Hb were shared with those generated by the related N. americanus cathepsin D, Na-APR-1. Antiserum against Na-APR-2 inhibited migration of 50% of third-stage N. americanus larvae through skin, which suggests that aspartic proteases might be effective vaccines against human hookworm disease.

Amino Acid Sequence↗
PubMed1995

Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR.

During the search for unknown factors involved in motility, we have found that expression of the flagellar master operon flhDC is affected by mutations of the pta and ackA genes, encoding phosphotransacetylase and acetate kinase, respectively (S. Shin, J. Sheen, and C. Park, Korean J. Microbiol. 31:504-511, 1993). Here we describe results showing that this effect is modulated by externally added acetate, except when both pta and ackA are mutated, suggesting the role of acetyl phosphate, an intermediate of acetate metabolism, as a regulatory effector. Furthermore, the following evidence indicates that the phosphorylation of OmpR, a trans factor for osmoregulation, regulates flagellar expression. First, in a strain lacking ompR, the expression of flhDC is no longer responsive to a change in the level of acetyl phosphate. Second, an increase in medium osmolarity does not decrease flhDC expression in an ompR mutant. It is known that such an increase normally enhances OmpR phosphorylation. Third, OmpR protein binds to the DNA fragment containing the flhDC promoter, and its affinity is increased with phosphorylation by acetyl phosphate. DNase I footprinting revealed the regions of the flhDC promoter protected by OmpR in the presence or absence of phosphorylation. Therefore, we propose that the phosphorylated OmpR, generated by either osmolarity change or the internal level of acetyl phosphate, negatively regulates the expression of flagella.

Acetates↗
PubMed1997

Ovarian- and somatic-specific transcripts of the mosquito clathrin heavy chain gene generated by alternative 5'-exon splicing and polyadenylation.

Insect oocytes are extraordinarily specialized for receptor-mediated endocytosis of yolk protein precursors. The clathrin heavy chain (CHC) is the major structural protein of coated vesicles, the principal organelles of receptor-mediated endocytosis. To understand the role of clathrin in the development of the oocyte's powerful endocytotic machinery we determined the structure of the mosquito chc gene. The gene spans approximately 45 kilobases and its coding region is divided into seven exons, five of which encode the protein. Three distinct mature transcripts of this gene were identified in mosquito tissues. Two of them code isoforms of the CHC polypeptide differing in their NH2-terminal sequences, and are specifically expressed in female germ-line cells. The third transcript has a 3'-untranslated region about 1 kilobase longer than the other variants, and is found only in the somatic cells. Tissue-specific 5'-exon splicing and alternative polyadenylation of the primary transcript combine to give rise to these mRNAs. We identified two alternative promoters, distal and proximal, separated by approximately 10 kilobases involved in tissue-specific regulation of mosquito chc gene expression. Our data provide the first molecular evidence for complex structure and regulation of a chc gene, in this case occurring at both the transcriptional and post-transcriptional levels.

Aedes↗
PubMed2001

High affinity binding of receptor-associated protein to heparin and low density lipoprotein receptor-related protein requires similar basic amino acid sequence motifs.

The 39-kDa receptor-associated protein (RAP) is a specialized chaperone for members of the low density lipoprotein receptor gene family, which also binds heparin. Previous studies have identified a triplicate repeat sequence within RAP that appears to exhibit differential functions. Here we generated a series of truncated and site-directed RAP mutants in order to define the sites within RAP that are important for interacting with heparin and low density lipoprotein receptor-related protein (LRP). We found that high affinity binding of RAP to heparin is mediated by the carboxyl-terminal repeat of RAP, whereas both the carboxyl-terminal repeat and a combination of amino and central repeats exhibit high affinity binding to LRP. Several motifs were found to mediate the binding of RAP to heparin, and each contained a cluster of basic amino acids; among them, an intact R(282)VSR(285)SR(287)EK(289) motif is required for high affinity binding of RAP to heparin, whereas two other motifs, R(203)LR(205)R(206) and R(314)ISR(317)AR(319), also contribute to this interaction. We also found that intact motifs of both R(203)LR(205)R(206) and R(282)VSR(285)SR(287)EK(289) are required for high affinity binding of RAP to LRP, with the third motif, R(314)ISR(317)AR(319), contributing little to RAP-LRP interaction. We conclude that electrostatic interactions likely contribute significantly in the binding of RAP to both heparin and LRP and that high affinity interaction with both heparin and LRP appears to require mostly overlapping sequence motifs within RAP.

Amino Acid Sequence↗
PubMed1993

The topology of the brown adipose tissue mitochondrial uncoupling protein determined with antibodies against its antigenic sites revealed by a library of fusion proteins.

The uncoupling protein (UCP) of brown adipose tissue mitochondria is a specialized member of the family of evolutionarily related mitochondrial membrane transporters, which also includes the ADP/ATP translocator and the phosphate carrier. We have generated a library of bacterial clones randomly expressing short subsequences of the UCP fused to the MalE periplasmic protein of Escherichia coli. Anti-UCP sera were used to select clones expressing antigenic sequences of the UCP. Ten different fusion proteins representing eight non-overlapping subsequences of the UCP were obtained. The ability of fusion proteins to select antibodies directed against a short segment of the UCP was used to study the topological organization of the UCP in the inner mitochondrial membrane. Four different fusion proteins were used to determine the orientation of the N-terminal extremities of the first, second, third and fourth predicted alpha-helices of the UCP. This topological study together with previous data on the UCP provides an experimental basis for the predicted structure of the UCP and for other homologous carrier proteins.

ATP-Binding Cassette Transporters↗
PubMed1998

Structure of the Drosophila projectin protein: isoforms and implication for projectin filament assembly.

The protein composition of the various muscle types in Drosophila melanogaster has been studied quite thoroughly and the analysis has revealed many differences involving the usage of muscle specific isoforms of a given protein, as well as the presence of proteins restricted to one muscle type. Drosophila projectin, the giant protein component of the third filament is quite unusual as it not only shows specific isoforms in various muscle types, but these isoforms are located at different sarcomeric locations, I band in the IFM and A band in synchronous muscles. This may suggest distinct functions for the projectin protein in various muscles, as well as a different set of protein interactions for each projectin isoform. Projectin is encoded by a single gene and the isoforms were proposed to be the result of alternative splicing of a primary transcript. Here, we report the nearly complete sequence of Drosophila projectin, as well as the possible splicing patterns used to generate different isoforms. The overall domain organization in projectin is composed of repeated motifs I and II in a few specific patterns, similar to its Caenorhabditis homolog, twitchin. Sequence similarity between twitchin and projectin further suggests how some domains may possibly be important for protein interactions and/or functions. Alternative splicing operates at the COOH terminus, leading to a shorter projectin protein lacking some of the terminal motifs II and unique sequence. These isoforms are discussed in view of projectin differential size and localization.

Alternative Splicing↗
PubMed1988

Electrophysiological analysis of the dorsal hippocampal commissure projections to the entorhinal area.

Synaptic effects evoked in the entorhinal area by dorsal hippocampal commissure (dorsal psalterium) projections were analysed in anesthetized adult guinea-pigs by means of a field potential analysis. Stimuli applied to the caudal part of the dorsal psalterium evoked a complex response in the dorsal third of the entorhinal area. The early part of the entorhinal response consisted of a slow wave interrupted by a spike potential. The electrophysiological characteristics and the laminar distribution of the slow wave and of the spike potential, together with the presence of time-locked unit activity, suggested that dorsal psalterium projections evoke monosynaptic excitatory postsynaptic potentials leading to cellular discharge in radially oriented neurons of layers II and III. The commissural fibers responsible for these effects originate in the contralateral presubiculum. The early part of the entorhinal response was followed by three waves in close temporal sequence. These waves were polysynaptically generated and associated with excitatory and inhibitory synaptic effects. Inhibition was demonstrated for the monosynaptically generated spike potential. Whether these effects were mediated by intracortical circuits and/or extrinsic projections cannot be stated from the present results. Causal relations were observed between the entorhinal monosynaptic response and that evoked by dorsal psalterium stimulation in the ipsilateral dentate gyrus, previously shown to be relayed by perforant path fibers. The results indicate that presubicular commissural projections to the entorhinal area monosynaptically activate neurons of the perforant pathway, whose discharge brings about activation of the ipsilateral dentate gyrus.

Action Potentials↗