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PubMed1995

Molecular and biochemical characterization of a Plasmodium falciparum cyclophilin containing a cleavable signal sequence.

The immunosuppressive drug cyclosporin A (CsA) inhibits the growth of malaria parasites in vitro and in vivo. Cyclosporin A exerts its immunosuppressive effect in T lymphocytes by binding to cyclophilin (CyP), a peptidylprolyl cis-trans isomerase (PPIase). It is believed that the cyclosporin/cyclophilin complex inhibits a Ca(2+)-activated protein phosphatase, calcineurin, involved in T-cell activation. A cDNA encoding a cyclophilin of the human malaria parasite Plasmodium falciparum has been isolated as a step in the elucidation of the mechanism of antimalarial action of CsA. This cDNA, termed PfCyP, encodes a protein of 195 amino acids which has highest similarity with the Candida albicans (73.1%) and the Drosophila melanogaster (73.1%) cytoplasmic cyclophilins. A Northern blot reveals an approximately 900-bp nucleotide transcript that is consistent with the predicted size of the encoded polypeptide. The predicted PfCyP protein has a putative endoplasmic-reticulum-directed signal sequence at its N-terminus and two potential N-linked glycosylation sites. Expression of PfCyP RNA in an in vitro translation/translocation system reveals that the PfCyP protein is translocated across microsomes, that the signal peptide is cleaved and that the PfCyP protein is glycosylated at two sites. The PfCyP cDNA open reading frame coding for the predicted mature protein has been expressed in Escherichia coli. The purified recombinant protein is an active PPIase (kcat/Km = 2.3 x 10(6) s-1 M-1); this enzymic activity is inhibited by CsA (IC50 = 10 nM). The PfCyP protein has thus the same sensitivity to CsA as the PPIase activity associated with P. falciparum extracts [Bell, A. et al. (1994) Biochem. Pharmacol. 48, 495-503] suggesting that PfCyP may be responsible for the PPIase activity in those extracts. If different cyclophilins exist in P. falciparum, we conclude that either the PfCyP protein is the major cyclophilin detected in the parasite or that there are other cyclophilins with similar susceptibilities to CsA.

Amino Acid Isomerases↗
PubMed2006

Lipoprotein computational prediction in spirochaetal genomes.

Lipoproteins are of great interest in understanding the molecular pathogenesis of spirochaetes. Because spirochaete lipobox sequences exhibit more plasticity than those of other bacteria, application of existing prediction algorithms to emerging sequence data has been problematic. In this paper a novel lipoprotein prediction algorithm is described, designated SpLip, constructed as a hybrid of a lipobox weight matrix approach supplemented by a set of lipoprotein signal peptide rules allowing for conservative amino acid substitutions. Both the weight matrix and the rules are based on a training set of 28 experimentally verified spirochaetal lipoproteins. The performance of the SpLip algorithm was compared to that of the hidden Markov model-based LipoP program and the rules-based algorithm Psort for all predicted protein-coding genes of Leptospira interrogans sv. Copenhageni, L. interrogans sv. Lai, Borrelia burgdorferi, Borrelia garinii, Treponema pallidum and Treponema denticola. Psort sensitivity (13-35 %) was considerably less than that of SpLip (93-100 %) or LipoP (50-84 %) due in part to the requirement of Psort for Ala or Gly at the -1 position, a rule based on E. coli lipoproteins. The percentage of false-positive lipoprotein predictions by the LipoP algorithm (8-30 %) was greater than that of SpLip (0-1 %) or Psort (4-27 %), due in part to the lack of rules in LipoP excluding unprecedented amino acids such as Lys and Arg in the -1 position. This analysis revealed a higher number of predicted spirochaetal lipoproteins than was previously known. The improved performance of the SpLip algorithm provides a more accurate prediction of the complete lipoprotein repertoire of spirochaetes. The hybrid approach of supplementing weight matrix scoring with rules based on knowledge of protein secretion biochemistry may be a general strategy for development of improved prediction algorithms.

Algorithms↗
PubMed2000

Assessing the predictive validity of frog embryo teratogenesis assay-Xenopus (FETAX).

The ability of frog embryo teratogenesis assay - Xenopus (FETAX) to identify the potential developmental toxicity of a group of diverse chemicals was evaluated by comparison with results from in vivo studies in rats. A total of 12 chemicals, three of which were shown to be teratogenic in vivo, four of which were embryolethal (but not teratogenic) in vivo, and five which did not produce any developmental toxicity in vivo in the rat were evaluated using FETAX. Results of the FETAX test with these 12 blind-coded compounds correctly predicted that three chemicals had strong teratogenic potential, four had low teratogenic hazard potential but were embryolethal, and five posed little if any developmental toxicity hazard. In addition, this study concluded that within a family of chemistry analogs could be ranked according to relative teratogenic hazard and that for the teratogenic compounds the types of malformations induced in Xenopus mimicked the abnormalities induced in vivo in rats. In summary, these results confirmed that the FETAX assay is predictive and can be useful in an integrated biological hazard assessment for the preliminary screening of chemicals. Teratogenesis Carcinog. Mutagen. 20:87-98, 2000.

Abnormalities, Drug-Induced↗
PubMed1999

Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction.

While genomic sequences are accumulating, finding the location of the genes remains a major issue that can be solved only for about a half of them by homology searches. Prediction methods are thus required, but unfortunately are not fully satisfying. Most prediction methods implicitly assume a unique model for genes. This is an oversimplification as demonstrated by the possibility to group coding sequences into several classes in Escherichia coli and other genomes. As no classification existed for Arabidopsis thaliana, we classified genes according to the statistical features of their coding sequences. A clustering algorithm using a codon usage model was developed and applied to coding sequences from A. thaliana, E. coli, and a mixture of both. By using it, Arabidopsis sequences were clustered into two classes. The CU1 and CU2 classes differed essentially by the choice of pyrimidine bases at the codon silent sites: CU2 genes often use C whereas CU1 genes prefer T. This classification discriminated the Arabidopsis genes according to their expressiveness, highly expressed genes being clustered in CU2 and genes expected to have a lower expression, such as the regulatory genes, in CU1. The algorithm separated the sequences of the Escherichia-Arabidopsis mixed data set into five classes according to the species, except for one class. This mixed class contained 89 % Arabidopsis genes from CU1 and 11 % E. coli genes, mostly horizontally transferred. Interestingly, most genes encoding organelle-targeted proteins, except the photosynthetic and photoassimilatory ones, were clustered in CU1. By tailoring the GeneMark CDS prediction algorithm to the observed coding sequence classes, its quality of prediction was greatly improved. Similar improvement can be expected with other prediction systems.

Algorithms↗
PubMed2005

A cDNA for a putative type III deiodinase in the trout (Oncorhynchus mykiss): influence of holding conditions and thyroid hormone treatment on its hepatic expression.

A putative rainbow trout type III deiodinase (D3) cDNA was amplified by PCR, using primers to evolutionarily conserved sequences. The RACE-derived complete cDNA was then identified by sequence comparison to that in tilapia and other vertebrates. The cDNA coded for a predicted 31,500 kDa protein of 278 amino acids, with a hydrophobic trans-membrane segment and with 80% similarity to tilapia D3 and 39% similarity to rainbow trout type II deiodinase (D2). It also showed a selenocysteine codon at position 141 and a putative SECIS element in the 3' untranslated end. In the liver, a second form of D3 was found that differed only at this 3' untranslated region; the coding region was identical in both forms. The D3 mRNA, measured by RT-PCR using primers located within the common, translated portion of the cDNA, was expressed in the brain and, depending on thyroidal status, in liver and kidney. Holding trout for 7 days in static water as opposed to flowing water caused increased plasma T4 levels, decreased hepatic D2 mRNA levels and T4 outer-ring deiodination (ORD) activity and increased D3 mRNA levels and T3 inner-ring (IRD) activity. Trout held in flowing water and fed T3 for 7 days showed increased plasma T3 levels and hepatic D3 mRNA levels and T3 IRD activity but decreased D2 mRNA levels and T4ORD activity. Trout held in static water and exposed to ambient T4 for 7 days showed increased plasma T4 levels and hepatic T3IRD activity but with no significant change in D2 or D3 mRNA levels. We conclude that hepatic D3 mRNA levels and T3IRD activity are enhanced and D2 mRNA levels and T4ORD activity are suppressed by adverse holding conditions or T3 treatment suggesting that the putative D3 cDNA and D2 cDNA represent respectively the genes determining T3IRD and T4ORD activities. However, there were changes in the ratios of mRNA levels to enzyme activity, raising the potential for post-transcriptional regulation and showing that mRNA levels alone may be unreliable indices of deiodinase activity. Post-transcriptional regulation of D3 enzyme activity may be influenced by the observed alternative 3' and 5' untranslated regions of the D3 mRNA.

Amino Acid Sequence↗
PubMed2003

Response priming by supraliminal and subliminal action effects.

Theories assuming an effect-based coding of action predict that motor responses become activated by the perception of the responses' sensory effects. In accordance with this prediction it was found that responding to a visual target is faster and more accurate when the target is briefly preceded by the visual effect of the required response. Most importantly, this effect-induced response priming was independent of prime perceptibility and it occurred even when the prime was not consciously discriminable. Beyond ruling out alternative interpretations of earlier induction studies in terms of deliberate response biases, this suggests that effect codes evoke their associated motor patterns in a highly automatic manner not affording conscious mediation. The results accord with a functional dissociation between the consciousness-mediated implementation and the consciousness-independent realization of action goals.

Humans↗
PubMed2003

mRNA 5' region sequence incompleteness: a potential source of systematic errors in translation initiation codon assignment in human mRNAs.

The amino acid sequence of gene products is routinely deduced from the nucleotide sequence of the relative cloned cDNA, according to the rules for recognition of start codon (first-AUG rule, optimal sequence context) and the genetic code. From this prediction stem most subsequent types of product analysis, although all standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. Revision by bioinformatics and cloning methods of 109 known genes located on human chromosome 21 (HC 21) shows that 60 mRNAs lack any in-frame stop upstream of the first-AUG, and that in five cases (DSCR1, KIAA0184, KIAA0539, SON, and TFF3) the coding region at the 5' end was incompletely characterized in the original descriptions. We describe the respective consequences for genomic annotation, domain and ortholog identification, and functional experiments design. We have also analyzed the sequences of 13,124 human mRNAs (RefSeq databank), discovering that in 6448 cases (49%), an in-frame stop codon is present upstream of the initiation codon, while in the other 6676 mRNAs (51%), identification of additional bases at the mRNA 5' region could well reveal some new upstream in-frame AUG codons in the optimal context. Proportionally to the HC 21 data, about 550 known human genes might thus be affected by this 5' end mRNA artifact.

5' Untranslated Regions↗
PubMed1977

Cytotoxic T lymphocytes induced against allogeneic I-region determinants react with Ia molecules on trinitrophenyl-conjugated syngeneic target cells.

The major histocompatibility complex codes for determinants which are recognized by and serve as targets for cytolytic T lymphocytes (CTL) (1). Antigens coded for by the K and D loci of the H-2 complex can activate xenogeneic or allogeneic CTL (2,3). In addition, the H-2K or H-2D gene products function as those molecules against which syngeneic CTL responses specific for chemical, viral, and minor H antigens are directed (4-8). It has recently been shown that Ia determinants can also serve as target antigens for distinct but weaker CTL responses (9-13). Those clones which recognize Ia antigens see them independently of K- or D- coded antigens as shown in genetic studies and by antisera-blocking experiments (12,13). We have proposed that the existence of clones of CTL specific for I-region-coded determinants is not fortuitous; rather these clones specifically recognize Ia determinants and may have an immunoregulatory role. These CTL may affect those immune functions which are at least partially dependent on or controlled by I-region-coded molecules. Two predictions can be made and tested concerning the role of Ia determinants in cytolytic systems and the role, if any, of I-region- specific CTL in regulating the immune response: (a) that if as we and others have shown, certain Ia specificities can serve as a third series of major histocompatibility antigens, then Ia antigens should be susceptible to the same types of antigenic modifications as H-2K- or H-2D-coded structures and thus serve as targets for CTL directed against modified-self in selected systems; and (b) that allogeneically induced I-region-specific CTL should demonstrate cross-reactivity with targets bearing modified syngeneic I-region-coded determinants. Data will be present which demonstrates that trinitrophenyl (TNP)-modified syngeneic I-region determinants can serve as targets for CTL induced by allogeneic Ia antigens.

Animals↗
PubMed2001

Purification, molecular cloning, and immunohistochemical localization of dipeptidyl peptidase II from the rat kidney and its identity with quiescent cell proline dipeptidase.

We purified dipeptidyl peptidase II (DPP II) to homogeneity from rat kidney and determined its physicochemical properties, including its molecular weight, substrate specificity, and partial amino acid sequence. Furthermore, we screened a rat kidney cDNA library, isolated the DPP II cDNA and determined its structure. The cDNA was composed of 1,720 base pairs of nucleotides, and 500 amino acid residues were predicted from the coding region of cDNA. Human quiescent cell proline dipeptidase (QPP) cloned from T-cells is a 58-kDa glycoprotein existing as a homodimer formed with a leucine zipper motif. The levels of amino acid homology were 92.8% (rat DPP II vs. mouse QPP) and 78.9% (rat DPP II vs. human QPP), while those of nucleotide homology were 93.5% (rat DPP II vs. mouse QPP) and 79.4% (rat DPP II vs. human QPP). The predicted amino acid sequences of rat DPP II and human and mouse QPP possess eight cysteine residues and a leucine zipper motif at the same positions. The purified DPP II showed similar substrate specificity and optimal pH to those of QPP. Consequently, it was thought that DPP II is identical to QPP. Northern blot analysis with rat DPP II cDNA revealed prominent expression of DPP II mRNA in the kidney, and the order for expression was kidney >> testis > or = heart > brain > or = lung > spleen > skeletal muscle > or = liver. In parallel with Northern blot analysis, the DPP II antigen was detected by immunohistochemical staining in the cytosol of epithelial cells in the kidney, testis, uterus, and cerebrum.

Amino Acid Sequence↗
PubMed2003

Gene prediction with a hidden Markov model and a new intron submodel.

MOTIVATION: The problem of finding the genes in eukaryotic DNA sequences by computational methods is still not satisfactorily solved. Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons. RESULTS: We have developed a new program, AUGUSTUS, for the ab initio prediction of protein coding genes in eukaryotic genomes. The program is based on a Hidden Markov Model and integrates a number of known methods and submodels. It employs a new way of modeling intron lengths. We use a new donor splice site model, a new model for a short region directly upstream of the donor splice site model that takes the reading frame into account and apply a method that allows better GC-content dependent parameter estimation. AUGUSTUS predicts on longer sequences far more human and drosophila genes accurately than the ab initio gene prediction programs we compared it with, while at the same time being more specific. AVAILABILITY: A web interface for AUGUSTUS and the executable program are located at http://augustus.gobics.de.

Algorithms↗
PubMed2026

hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.

MOTIVATION: Enrichment analysis is a cornerstone of "omics" data interpretation, enabling researchers to connect analysis results to biological processes and generate testable hypotheses. Enrichment analysis in metabolomics poses distinct challenges for interpretation and multi-omics integration due to the lack of well-defined and consistent connections to well-curated gene-centered biological knowledge repositories. To address these challenges, we developed hypeR-GEM, a methodology and associated R package that adapts gene set enrichment analysis to metabolomics. hypeR-GEM leverages genome-scale metabolic models (GEMs) to infer reaction-based links between metabolites and enzyme-coding genes, enabling the mapping of metabolite signatures to gene signatures and their subsequent annotation via gene set enrichment analysis. RESULTS: We validated hypeR-GEM using paired metabolomics-proteomics and metabolomics-transcriptomics datasets by assessing whether genes mapped from metabolites significantly overlapped with differentially expressed proteins or transcripts. We further evaluated whether pathways enriched via hypeR-GEM-mapped genes corresponded to those derived from paired proteomic or transcriptomic data. In most datasets analyzed, both the predicted enzyme-coding genes and the associated enriched pathways showed significant concordance with independently derived omics signatures, supporting the utility and robustness of hypeR-GEM. Finally, we applied hypeR-GEM to the analysis of age-associated metabolic signatures from the New England Centenarian Study. The results revealed consistent enrichment of lipid-related pathways, aligning with the well-established role of lipid metabolism in aging, and highlighted additional pathways not captured in the metabolites' annotation, demonstrating hypeR-GEM's practical utility in a real-world use case. AVAILABILITY AND IMPLEMENTATION: The hypeR-GEM R package, documentation, and workflow examples are freely available at https://github.com/montilab/hypeR-GEM and archived at https://doi.org/10.5281/zenodo.20586748.

Metabolomics↗
PubMed1994

The organization of intercistronic regions of the aerobactin operon of pColV-K30 may account for the differential expression of the iucABCD iutA genes.

The complete nucleotide sequence of the 8.3 kilobase operon of the enterobacterial virulence plasmid pColV-K30, which encodes a high-affinity iron transport system mediated by the hydroxamate siderophore aerobactin, has been determined. The region includes five open reading frames which correspond to the genes iucA, iucB, iucC and iucD, encoding the enzymes of the biosynthetic pathway for aerobactin, and iutA for the outer membrane receptor of ferri-aerobactin complexes. The sequences of the iucABCD genes are tightly coupled without any intervening non-coding sequence. The predicted secondary mRNA structures at the gene junctions within the iucABCD cluster, along with their codon usage, may account for the differential expression of each of the protein products, as observed in vivo with minicells. The genes iucA and iucC, which determine the two subunits of the aerobactin synthetase complex, showed a considerable homology within three stretches of their amino acid sequence. A potential operator sequence (iron box) for the binding of the iron(II)-responsive Fur repressor protein was found within the iucA coding region, suggesting that the operon is subjected to an additional level of transcriptional repression by iron (II).

Amino Acid Sequence↗
PubMed2000

A recurrent model of transformation invariance by association.

This paper describes an investigation of a recurrent artificial neural network which uses association to build transform-invariant representations. The simulation implements the analytic model of Parga and Rolls [(1998). Transform-invariant recognition by association in a recurrent network. Neural Computation 10(6), 1507-1525.] which defines multiple (e.g. "view") patterns to be within the basin of attraction of a shared (e.g. "object") representation. First, it was shown that the network could store and correctly retrieve an "object" representation from any one of the views which define that object, with capacity as predicted analytically. Second, new results extended the analysis by showing that correct object retrieval could occur where retrieval cues were distorted; where there was some association between the views of different objects; and where connectivity was diluted, even when this dilution was asymmetric. The simulations also extended the analysis by showing that the system could work well with sparse patterns; and showing how pattern sparseness interacts with the number of views of each object (as a result of the statistical properties of the pattern coding) to give predictable object retrieval performance. The results thus usefully extend a recurrent model of invariant pattern recognition.

Artificial Intelligence↗
PubMed2006

Performance of International Classification Of Diseases, 9th Revision, Clinical Modification codes as an adverse drug event surveillance system.

BACKGROUND: Adverse drug events (ADEs) are one of the most frequent causes of iatrogenic injury. Because International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM) codes are routinely assigned to inpatient discharges, they could provide a method to detect ADEs within a hospital, a state, and the nation. OBJECTIVE: The objective of this study was to determine validity of selected ICD-9-CM codes in identifying inpatient ADEs. RESEARCH DESIGN: An expert panel identified 416 ICD-9-CM codes to represent ADEs (flagged ADE codes). Retrospective chart review using a structured tool was performed to ascertain code performance in detecting ADEs. SUBJECTS: Subjects included 3103 inpatients from all 41 acute care hospitals in Utah in 2001: 1961 inpatients sampled randomly (random sample) and 1142 inpatients sampled from the discharge records with at least one flagged ADE code (flagged sample). MEASURES: Measures were ADEs identified by structured review. RESULTS: The flagged sample yielded 1122 flagged ADE codes recorded in patient charts with 704 representing ADEs (63%). Two hundred eighty-six of the 704 verified ADE codes (41%) were determined to be inpatient ADEs. In the random sample, 32 of 58 ADEs (55%) causing hospital admission were detected by the ADE-flagged codes. Only 23 of 224 inpatient ADEs had been assigned a flagged ADE code (10%). CONCLUSIONS: Flagged ADE codes have an overall positive predictive value of 63% and detect just over half of ADEs causing hospital admission. These codes have a positive predictive value of 25% for inpatient ADEs but detect only 10% of overall inpatient ADEs. Flagged ADE codes provide an imperfect but immediately available ADE surveillance system.

Adverse Drug Reaction Reporting Systems↗
PubMed2004

Human midbrain sensitivity to cognitive feedback and uncertainty during classification learning.

Mesencephalic dopaminergic system (MDS) neurons may participate in learning by providing a prediction error signal to their targets, which include ventral striatal, orbital, and medial frontal regions, as well as by showing sensitivity to the degree of uncertainty associated with individual stimuli. We investigated the mechanisms of probabilistic classification learning in humans using functional magnetic resonance imaging to examine the effects of feedback and uncertainty. The design was optimized for separating neural responses to stimulus, delay, and negative and positive feedback components. Compared with fixation, stimulus and feedback activated brain regions consistent with the MDS, whereas the delay period did not. Midbrain activity was significantly different for negative versus positive feedback (consistent with coding of the "prediction error") and was reliably correlated with the degree of uncertainty as well as with activity in MDS target regions. Purely cognitive feedback apparently engages the same regions as rewarding stimuli, consistent with a broader characterization of this network.

Adult↗
PubMed2002

A novel theory on the origin of the genetic code: a GNC-SNS hypothesis.

We have previously proposed an SNS hypothesis on the origin of the genetic code (Ikehara and Yoshida 1998). The hypothesis predicts that the universal genetic code originated from the SNS code composed of 16 codons and 10 amino acids (S and N mean G or C and either of four bases, respectively). But, it must have been very difficult to create the SNS code at one stroke in the beginning. Therefore, we searched for a simpler code than the SNS code, which could still encode water-soluble globular proteins with appropriate three-dimensional structures at a high probability using four conditions for globular protein formation (hydropathy, alpha-helix, beta-sheet, and beta-turn formations). Four amino acids (Gly [G], Ala [A], Asp [D], and Val [V]) encoded by the GNC code satisfied the four structural conditions well, but other codes in rows and columns in the universal genetic code table do not, except for the GNG code, a slightly modified form of the GNC code. Three three-amino acid systems ([D], Leu and Tyr; [D], Tyr and Met; Glu, Pro and Ile) also satisfied the above four conditions. But, some amino acids in the three systems are far more complex than those encoded by the GNC code. In addition, the amino acids in the three-amino acid systems are scattered in the universal genetic code table. Thus, we concluded that the universal genetic code originated not from a three-amino acid system but from a four-amino acid system, the GNC code encoding [GADV]-proteins, as the most primitive genetic code.

Alanine↗
PubMed1994

The cobC gene of Salmonella typhimurium codes for a novel phosphatase involved in the assembly of the nucleotide loop of cobalamin.

We report the identification of a new locus, designated cobC, involved in the assembly of the nucleotide loop of cobalamin in Salmonella typhimurium. The cobC gene has been mapped, cloned, and sequenced. DNA sequence analysis suggested that cobC is divergently transcribed from the adjacent cobD gene and suggests that the regulatory region of these genes overlap. The cobC gene codes for a predicted polypeptide of 26 kDa with striking homology to phosphoglycerate mutase, fructose-2,6-bisphosphatase, and acid phosphatase enzymes. In vitro experiments demonstrated that CobC dephosphorylated the cobalamin biosynthetic intermediate N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole to generate N1-alpha-D-ribosyl-5,6-dimethylbenzimidazole. In vivo data showed that the lack of cobC function blocks the synthesis of cobalamin from its precursors cobinamide and 5,6-dimethylbenzimidazole, i.e. it prevents the assembly of the nucleotide loop of cobalamin. Additionally, exogenous N1-alpha-D-ribosyl-5,6-dimethylbenzimidazole rescues the defect of a cobC mutant. We propose that cobC codes for a novel phosphatase whose primary role is in cobalamin biosynthesis. A model for the sequence of biosynthetic steps that assemble the nucleotide loop of cobalamin in S. typhimurium is presented.

Amino Acid Sequence↗
PubMed1990

Characterization and expression of a glycoprotein encoded by the Epstein-Barr virus BamHI I fragment.

Computer-assisted analysis of the Epstein-Barr virus (EBV) open reading frame BILF2 (B95-8 nucleotides 150,525 to 149,782) predicts that it codes for a membrane-bound glycoprotein. [3H]glucosamine labeling of cells infected with vaccinia virus recombinants that expressed the BILF2 open reading frame revealed several diffuse species of glycoproteins of around 80,000 and 55,000 daltons. A monoclonal antibody derived from spleens of mice immunized with EBV immunoprecipitated the EBV-derived protein made by the vaccinia virus recombinants and also precipitated a late envelope glycoprotein with a mobility of 78,000 to 55,000 from EBV-producing cells. N-Glycanase treatment of the immunoprecipitated BILF2 product from EBV-producing cells resulted in a polypeptide of 28 kilodaltons, closely agreeing with the predicted molecular mass for the unmodified BILF2 gene product. Western (immuno-) blots using recombinant infected cells as a source of antigen showed that the majority of EBV-seropositive individuals have a serum antibody response to the BILF2-encoded gp78/55.

Amino Acid Sequence↗