DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages.

We have determined the DNA sequence of the bacteriophage P2 tail genes G and H, which code for polypeptides of 175 and 669 residues, respectively. Gene H probably codes for the distal part of the P2 tail fiber, since the deduced sequence of its product contains regions similar to tail fiber proteins from phages Mu, P1, lambda, K3, and T2. The similarities of the carboxy-terminal portions of the P2, Mu, ann P1 tail fiber proteins may explain the observation that these phages in general have the same host range. The P2 H gene product is similar to the products of both lambda open reading frame (ORF) 401 (stf, side tail fiber) and its downstream ORF, ORF 314. If 1 bp is inserted near the end of ORF 401, this reading frame becomes fused with ORF 314, creating an ORF that may represent the complete stf gene that encodes a 774-amino-acid-long side tail fiber protein. Thus, a frameshift mutation seems to be present in the common laboratory strain of lambda. Gene G of P2 probably codes for a protein required for assembly of the tail fibers of the virion. The entire G gene product is very similar to the products of genes U and U' of phage Mu; a region of these proteins is also found in the tail fiber assembly proteins of phages TuIa, TuIb, T4, and lambda. The similarities in the tail fiber genes of phages of different families provide evidence that illegitimate recombination occurs at previously unappreciated levels and that phages are taking advantage of the gene pool available to them to alter their host ranges under selective pressures.     

Analysis of a bacterial hygromycin B resistance gene by transcriptional and translational fusions and by DNA sequencing

We have characterized hygromycin B and apramycin resistance genes from an E. coli plasmid. We have localized the coding and control regions of these genes by deletion of DNA fragments from plasmids containing the genes. It was found that polypeptides with apparent molecular weights of 33,000 and 31,500 daltons are encoded by the apramycin resistance gene and polypeptides with apparent molecular weights of 42,500 and 41,500 daltons are encoded by the hygromycin B resistance gene. DNA sequence analysis identified a typical promoter sequence upstream of the genes. Deletion of this promoter eliminated both resistance phenotypes, and hygromycin B resistance could be restored by substitution of a promoter from a foreign gene. The region known to be necessary for hygromycin B resistance contained an open reading frame large enough to encode the hygromycin B resistance gene product. This open reading frame was fused with the amino terminus of beta-galactosidase. This hybrid gene conferred hygromycin resistance to E. coli, and expression of resistance was under IPTG control.     

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.     

Sequence analysis of the gtfB gene from Streptococcus mutans.

The nucleotide sequence of the gtfB gene from Streptococcus mutans GS-5, coding for glucosyltransferase I activity, was determined. The gene codes for a strongly hydrophilic protein with a molecular size of 165,800 daltons. The deduced amino acid sequence revealed a typical gram-positive bacterial signal sequence at the NH2 terminus of the protein and 3.5 direct repeating units (each containing 65 amino acids) at the COOH terminus. Nucleotide sequencing of the region immediately downstream from the gtfB gene revealed the presence of a putative gene coding for an extracellular protein. This open reading frame is partially homologous to the gtfB gene.     

Reovirus type 3 genome segment S4: nucleotide sequence of the gene encoding a major virion surface protein

A full-length cDNA copy of reovirus double-stranded RNA genome segment S4 which codes for a major virion structural polypeptide, sigma 3, has been completely sequenced. The 1,196-nucleotide cDNA contains a single long open reading frame in the plus strand extending 1,095 nucleotides from the 5'-proximal A-T-G to a single stop codon. This corresponds to translation of 92% of the S4 gene. The inferred sigma 3 polypeptide is hydrophilic and consists of 365 amino acids, totalling 41,164 daltons.     

Cloning and expression of the aspartate carbamoyltransferase gene from Treponema denticola.

Treponema denticola seems to play a central role in the etiology of human periodontal disease. We have cloned an antigenic protein-coding sequence from T. denticola ATCC 33520. The protein-coding region was found to be a 3-kbp HindIII-HindIII fragment. The open reading frame consists of 1,426 bp and codes for a protein with an M(r) of 54,919. The deduced amino acid sequence showed 33.8% homology with that of the aspartate carbamoyltransferase of Escherichia coli. The gene products showed aspartate carbamoyltransferase activity.     

Isolation and analysis of the genes for cytochrome c oxidase in Paracoccus denitrificans

Synthetic oligonucleotide probes were used to clone two loci from the chromosomal DNA of Paracoccus denitrificans that contain the genes for cytochrome c oxidase (cytochrome aa₃). One locus seems to contain four or five genes probably forming an operon. Two of these code for the oxidase subunits II and III. Three open reading frames are found between the COII and COIII genes. The other locus codes for the subunit I. A short open reading frame is found upstream of this gene. All three subunits of the Paracoccus enzyme show remarkable homology to the corresponding subunits of the mitochondrial cytochrome oxidase. Possible protein products of the open reading frames have not yet been identified.     

Cloning and expression of the aspartate carbamoyltransferase gene from Treponema denticola.

Treponema denticola seems to play a central role in the etiology of human periodontal disease. We have cloned an antigenic protein-coding sequence from T. denticola ATCC 33520. The protein-coding region was found to be a 3-kbp HindIII-HindIII fragment. The open reading frame consists of 1,426 bp and codes for a protein with an M(r) of 54,919. The deduced amino acid sequence showed 33.8% homology with that of the aspartate carbamoyltransferase of Escherichia coli. The gene products showed aspartate carbamoyltransferase activity.     

Identification of the murine Mx2 gene: interferon-induced expression of the Mx2 protein from the feral mouse gene confers resistance to vesicular stomatitis virus

The mouse genome contains two related interferon-regulated genes, Mx1 and Mx2. Whereas Mx1 codes for the nuclear 72-kDa protein that interferes with influenza virus replication after interferon treatment, the Mx2 gene is nonfunctional in all laboratory mouse strains examined, since its open reading frame (ORF) is interrupted by an insertional mutation and a subsequent frameshift mutation. In the present study, we demonstrate that Mx2 mRNA of cells from feral mouse strains NJL (Mus musculus musculus) and SPR (Mus spretus) differs from that of the laboratory mouse strains tested. The Mx2 mRNA of the feral strains contains a single long ORF consisting of 656 amino acids. We further show that Mx2 protein in the feral strains is expressed upon interferon treatment and localizes to the cytoplasm much like the rat Mx2 protein, which inhibits vesicular stomatitis virus replication. Furthermore, transfected 3T3 cell lines of laboratory mouse origin expressing Mx2 from feral strains acquire slight resistance to vesicular stomatitis virus.     

Comparison of the maxicircle (mitochondrial) genomes of Leishmania tarentolae and Trypanosoma brucei at the level of nucleotide sequence

The entire 16.7-kilobase (kb) transcribed region of the Leishmania tarentolae maxicircle was compared to the entire 15-kb transcribed region of the Trypanosoma brucei maxicircle at the nucleotide sequence level by dot matrix analysis and by alignments of individual genes. The L. tarentolae NADH dehydrogenase subunit 1 (ND1) gene was identified in a newly obtained 2.9-kb sequence. All but two regions which flank the cytochrome b gene are highly conserved in both species. One 3.1-kb region in L. tarentolae that contains the cytochrome oxidase subunit III (COIII) gene and several open reading frames corresponds to a 2-kb sequence in T. brucei with limited sequence homology that lacks the COIII gene. Another 0.6-kb region that comprises an unidentified open reading frame (open reading frame 12) in L. tarentolae is substituted by a nonhomologous 0.4-kb open reading frame in T. brucei. A short intergenic region between the ND1 gene and the maxicircle unidentified reading frame 1 gene shows limited sequence homology, and the regions between the ND4 and ND5 genes and between the COI and ND4 genes are not conserved. All of the intergenic regions share G + C richness and a similar pattern of G versus C strand bias. 1.8 kb of the L. tarentolae divergent region (DV) and around 3 kb of the T. brucei DV were also obtained. The T. brucei DV sequences were not homologous to the L. tarentolae DV sequence but were organized in a similar fashion with tandem repeats of varying complexity.     

Nucleotide sequence of the gene and features of the major outer membrane protein of a virulent Rickettsia prowazekii strain.

We have determined the nucleotide sequence of the gene for a major outer membrane protein (MOMP) of apparent molecular weight 29.5 kD of the virulent Breinl strain of Rickettsia prowazekii. The gene contains an open reading frame (ORF) that encodes a 282-amino-acid polypeptide with a calculated molecular mass of 31549 daltons. A signal-like peptide sequence is found at the deduced N terminus. A heterologous 29.5-kD antigen expressed in Escherichia coli was shown to be secreted into the periplasm. A database search for similar protein sequences revealed considerable homology of the polypeptide with the E. coli peptidyl-prolyl cis/trans isomerase and related proteins of the parvulin family. The genes for MOMP of the virulent Breinl and EVir strains and the vaccine Madrid E strain were amplified using specific primers and cloned into expression vector pQE-30. We found that the polypeptides encoded by the recombinant DNAs do not differ in SDS-PAGE mobility, while the native MOMP of the Breinl strain is known to be different from the corresponding proteins of the Madrid E and EVir strains. Furthermore, no differences within the ORF for the 29.5-kD proteins of the three strains were found by restriction endonuclease analysis of polymerase chain reaction (PCR) products. A possible role of parvulin-like protein (Plp) in the virulence of epidemic typhus agent and the nature of interstrain differences are discussed. Near the plp gene on the opposite strand, an origin of the gene that codes for the SecA subunit of a preprotein translocase was found.     

Cloning of the human RoDH-related short chain dehydrogenase gene and analysis of its structure

We have previously characterized the first human NAD(+)-dependent short chain dehydrogenase capable of oxidizing all-trans-retinol and androgens, and found only in the liver and skin. In a search for related human enzymes, we identified a partial open reading frame, which exhibited >60% sequence identity to human RoDH-4. The full-length cDNA for this enzyme was determined in our laboratory by 5'-RACE PCR and was found to be identical to the recently reported novel type of oxidative human 3alpha-hydroxysteroid dehydrogenase (3alpha-HSD). Analysis of the genomic structure revealed that the gene for RoDH-like 3alpha-HSD has four translated exons and, possibly, a fifth exon that codes for the 5'-untranslated region. The gene for RoDH-4 appears to have only four exons. The positions of exon-intron boundaries and the sizes of the protein coding regions are identical in 3alpha-HSD and RoDH-4. Moreover, both genes are mapped to chromosome 12q13, and are located in a close proximity to each other. Both genes appear to have satellite pseudogenes. Thus, RoDH-4 and 3alpha-HSD genes share similar structural organization and cluster on human chromosome 12, near the gene for 11-cis retinol dehydrogenase.