Incomplete Open Reading Frames Research Articles

Evidence for a mosaic structure of the Tn5481 in Lactococcus lactis N8.

The sequences of the left end of the nisin-sucrose transposon Tn5481 in Lactococcus lactis subsp. lactis N8, the adjacent 1.5 kb chromosomal region upstream of the junction site as well as a 5.0 kb region downstream of the nisZBTCIPRKFEG genes within the transposon have been determined. In the upstream chromosomal region, an incomplete open reading frame encoding a protein with strong N-terminal homology to the low-affinity branched chain amino acid carriers was identified. Within the transposon, downstream of the nisin gene cluster, a 186 bp almost identical copy of the left hand sequence was located. Further downstream, four new open reading frames were found. The codon usage in these reading frames as well as the G+C content of the region are clearly different from those of the nisin genes, suggesting that the functionally unrelated areas of Tn5481 are gathered from different origins during the evolution of the transposon.

Isolation of a functional ecdysteroid receptor homologue from the ixodid tick Amblyomma americanum (L.)

Ecdysteroids are assumed to be the major steroid hormones in arthropods. However, with the exception of insects and crustaceans, very little is known about ecdysteroid action in other arthropods. To determine if ecdysteriods play a functional role in the ixodid tick, Amblyomma americanum (L.), we isolated cDNAs encoding three presumed ecdysteroid receptor isoforms (AamEcRA1, AamEcRA2, and AamEcRA3) that have common DNA and ligand binding domains linked to distinct amino termini. The DNA and ligand binding domains share an average of 86 and 64% identity, respectively with DNA and ligand binding domains from insect EcR proteins. The amino termini are highly divergent and the AamEcRs lack the `F' domain found in the insect EcRs. Analysis of AamEcR cDNAs show that processing of the AamEcR gene is complex, producing multiple transcripts with unique 5′ and 3′ termini as well as splicing variants with incomplete open reading frames. AamEcR mRNA profiles in whole animals and isolated tissues are consistent with complex regulation of AamEcR expression. We also examined the ability of AamEcRA1, when paired with an AamRXR, to activate transcription of an ecdysone response element containing reporter, and demonstrate that the AamEcR gene encodes a functional ecdysteroid receptor.

Sequence of a melibiose transporter gene of Enterobacter cloacae

We cloned a fragment of the chromosomal DNA of Enterobacter cloacae, which enabled a melibiose-negative Escherichia coli mutant lacking melB to grow on melibiose as the sole source of carbon. Transformed cells harboring the hybrid plasmid carrying the cloned DNA showed melibiose transport activity. The nucleotide sequence of the DNA region was determined. One complete open reading frame (ORF) and a part of another ORF were found in the region, and the amino acid sequences were deduced. The complete ORF was found to encode a melibiose transporter which consisted of 425 amino acid residues. Hydropathy analysis revealed that there are about 12 hydrophobic domains in this transporter. The incomplete ORF which exists in the upstream region of the transporter gene seemed to encode an α-galactosidase.

Cloning and characterization of sulfite dehydrogenase, two c-type cytochromes, and a flavoprotein of Paracoccus denitrificans GB17: essential role of sulfite dehydrogenase in lithotrophic sulfur oxidation.

A 13-kb genomic region of Paracoccus dentrificans GB17 is involved in lithotrophic thiosulfate oxidation. Adjacent to the previously reported soxB gene (C. Wodara, S. Kostka, M. Egert, D. P. Kelly, and C. G. Friedrich, J. Bacteriol. 176:6188-6191, 1994), 3.7 kb were sequenced. Sequence analysis revealed four additional open reading frames, soxCDEF. soxC coded for a 430-amino-acid polypeptide with an Mr of 47,339 that included a putative signal peptide of 40 amino acids (Mr of 3,599) with a RR motif present in periplasmic proteins with complex redox centers. The mature soxC gene product exhibited high amino acid sequence similarity to the eukaryotic molybdoenzyme sulfite oxidase and to nitrate reductase. We constructed a mutant, GBsoxC delta, carrying an in-frame deletion in soxC which covered a region possibly coding for the molybdenum cofactor binding domain. GBsoxC delta was unable to grow lithoautotrophically with thiosulfate but grew well with nitrate as a nitrogen source or as an electron acceptor. Whole cells and cell extracts of mutant GBsoxC delta contained 10% of the thiosulfate-oxidizing activity of the wild type. Only a marginal rate of sulfite-dependent cytochrome c reduction was observed from cell extracts of mutant GBsoxC delta. These results demonstrated that sulfite dehydrogenase was essential for growth with thiosulfate of P. dentrificans GB17. soxD coded for a periplasmic diheme c-type cytochrome of 384 amino acids (Mr of 39,983) containing a putative signal peptide with an Mr of 2,363. soxE coded for a periplasmic monoheme c-type cytochrome of 236 amino acids (Mr of 25,926) containing a putative signal peptide with an Mr of 1,833. SoxD and SoxE were highly identical to c-type cytochromes of P. denitrificans and other organisms. soxF revealed an incomplete open reading frame coding for a peptide of 247 amino acids with a putative signal peptide (Mr of 2,629). The deduced amino acid sequence of soxF was 47% identical and 70% similar to the sequence of the flavoprotein of flavocytochrome c of Chromatium vinosum, suggesting the involvement of the flavoprotein in thiosulfate oxidation of P. denitrificans GB17.

Investigation of different recombinant isoforms of grass group-V allergens (timothy grass pollen) isolated by low-stringency cDNA hybridization--antibody binding capacity and allergenic activity.

A cDNA library of timothy grass pollen was screened for homologous isoforms of major group-V allergens by low stringency hybridization with a Phl p 5 (Phleum pratense) probe. After restriction analysis of the 40 clones obtained, 17 were selected for cDNA sequencing. Of these clones, two were unrelated to group-V allergens, six showed high similarity but an incomplete open reading frame and nine had high similarity with a complete open reading frame. Comparison of deduced amino acids of ten complete cDNA clones confirmed the presence of two major isoforms, a and b. Within these two subgroups, only minor sequence variations were observed. Eight isoforms were expressed in Escherichia coli K12 and purified to homogeneity. Although the subgroups a and b could be distinguished by their molecular masses and by binding constants towards monoclonal antibodies, all isoforms turned out to be biochemically similar. Ribonuclease activity as a marker for the biological function of group-V allergens was shown to be in the same range for both subgroups. Analysis of allergenic B-cell responses towards the isoforms in 26 grass pollen allergic patients revealed that the IgE reactivities to the different isoforms were identical for each individual. IgE reactivities and allergenic activities of three isovariants and an allergen of a different group were compared in a selected group of four grass pollen allergic patients by immunoblot, histamine-release and skin-prick tests. The IgE reactivity does not necessarily mirror the allergenic activity of the single molecule, and the variability of allergenic activity between the isovariants does not, in every case, depend on the structural differences of these allergens. We conclude that group-V isoallergens in grass pollen, although they can be structurally different, induce a similar B-cell response but can show variable allergenic activity. Thus, the most allergenic isoform of each important group of allergens should be sufficient for the diagnosis of type-I allergy. Whether the isoallergenic variation has any significant influence on the outcome of immunotherapy in allergic disease still has to be elucidated.

Identification of the CD45-associated 116-kDa and 80-kDa Proteins as the α- and β-Subunits of α-Glucosidase II

CD45 is an abundant, highly glycosylated transmembrane protein-tyrosine phosphatase expressed on hematopoietic cells. Herein we demonstrate that two proteins of 116 kDa and 80 kDa copurify with CD45 from mouse T cells. Microsequence analysis of the 116-kDa protein revealed high similarity to an incomplete human open reading frame that has been suggested to correspond to the catalytic alpha-subunit of glucosidase II. We determined the nucleotide sequence of the mouse cDNA and observed that it encodes a protein product nearly identical to its human homologue and shares an active site consensus sequence with Family 31 glucosidases. Amino acid sequencing of the 80-kDa protein, followed by molecular cloning, revealed high homology to human and bovine cDNAs postulated to encode the beta-subunit of glucosidase II. Antisera developed to the mouse beta-subunit allowed us to demonstrate that the interaction between CD45 and glucosidase II can be reconstituted in vitro in an endoglycosidase H-sensitive manner. The strong interaction between glucosidase II and CD45 may provide a paradigm for investigating novel aspects of the biology of these proteins.

Sequence analysis of a 10.5 kb DNA fragment from the yeast chromosome VII reveals the presence of three new open reading frames and of a tRNAThr gene.

We report the sequence analysis of a 10,531 bp DNA of Saccharomyces cerevisiae chromosome VII. This sequence contains five complete open reading frames (ORFs) potentially encoding proteins longer than 100 amino acids and incomplete ORF encoding for the 3' part of the GCN5 gene (Georgakopoulos and Thireos, 1992). ORFs G9160 and G9155 correspond to the genes ENO1 (Holland et al. 1981) and PUP2 (Gergatsou et al., 1992) respectively. ORF G9165 codes for a protein which shares significant homology with known proteins present in databases (see below). The translated sequence of ORF G9170 shows 88% identity to the 6-phosphogluconate dehydrogenase encoded by the gene 6PGD from S. cerevisiae present in the SwissProt data library (P38720). This indicates that G9170 might code for a second 6-phosphogluconate dehydrogenase. ORF G9175 codes for a putative new member of the mitochondrial carrier family. A hypothetical tRNAThr (TGT) is also present in position 6842-6913.

Molecular analysis of the cos region of the Lactobacillus casei bacteriophage A2. Gene product 3, gp3, specifically binds to its downstream cos region.

The terminal nucleotide sequence of the Lactobacillus casei bacteriophage A2 DNA revealed a single-stranded extension 13 bases in length (5'-AACGGTCGGCCTC-3') at its 3' termini that defines the packaging initiation nicking site (cosN). The cosN sequence is bisected by an axis of hyphenated twofold rotational symmetry. Directly and inverted repeated sequences located to the left (cosL) and the right (cosR) of the cosN site were observed. Analysis of the 3.4 kb EcoRI DNA sequence surrounding the cos region revealed four complete and one incomplete open reading frames (orfs). Northern blots indicated that all were cotranscribed in a single mRNA molecule in excess of 10 kb that appeared late during infection. Minicell studies indicated that the four orfs were translated into protein. From the ORF3 amino acid sequence DNA-binding and NTP-binding domains can be predicted. The purified ORF3 (predicted molecular mass 16.8 kDa) shows specific binding to the A2 cos region, so it was renamed gp3. Gp3 forms a specific complex with a 369 bp cos DNA segment in the presence of ATP. Gp3 interaction with the intrinsically bent cos DNA segment induces intramolecular ligation in the presence of T4 DNA ligase. The data presented here suggest that gp3 is the small subunit of the terminase enzyme.

Molecular characterization of the xerC gene of Lactobacillus leichmannii encoding a site-specific recombinase and two adjacent heat shock genes.

Sequencing of four overlapping DNA fragments comprising 3.527 kb isolated from a L. leichmannii genomic library revealed three complete open reading frames (ORFs) and one that was truncated. The deduced amino acid sequences of the complete ORFs showed considerable similarities with the already known sequences of the xerC, hslV, and hslU gene products of Escherichia coli: the site-specific XerC recombinase, a member of the lambda integrase family, and the HtpI resp. HtpO heat shock proteins. The deduced amino acid sequence of the fourth, incomplete ORF upstream the xerC gene showed strong homology with the gid A gene product of B. subtilis.

Sequence analysis of a 10 kb DNA fragment from yeast chromosome VII reveals a novel member of the dnaJ family

We report the sequence analysis of a 10 kb DNA fragment of Saccharomyces cerevisiae chromosome VII. This sequence contains four complete open reading frames (ORFs) of greater than 100 amino acids. There are also two incomplete ORFs flanking the extremes: one of these, G2868, is the 5' part of the SCS3 gene (Hosaka et al., 1994). ORFs G2853 and G2856 correspond to the genes CEG1, coding for the alfa subunit of the mRNA guanylyl transferase and a 3' gene of unknown function previously sequenced (Shibagaki et al., 1992). G2864 is identical to SOH1 also reported (Fan and Klein, 1994).

Characterisation of genes involved in biosynthesis of coronafacic acid, the polyketide component of the phytotoxin coronatine

Coronafacic acid (CFA) is the polyketide component of coronatine (COR), a phytotoxin produced by the plant pathogen, Pseudomonas syringae. In the present study we have determined the nucleotide sequence of a 3.92-kb DNA fragment involved in CFA biosynthesis. Analysis of the sequence revealed four complete open reading frames (ORFs) designated cfal to cfa4 and one incomplete ORF ( cfa5), all transcribed in the same direction. The predicted translation products of cfal, cfa2 and cfa3 showed relatedness to acyl carrier proteins, fatty acid dehydrases and β-ketoacylsynthases, respectively, which are required for polyketide synthesis. cfal was subcloned, its sequence was confirmed, and it was overexpressed in E. coli to yield a peptide with an apparent molecular mass of 6 kDa.

Cloning and characterization of the Bacillus subtilis prkA gene encoding a novel serine protein kinase

We have cloned and sequenced a 3574-bp Bacillus subtilis (Bs) DNA fragment located between the nrdA and citB genes at about 169° on the chromosome. An Escherichia coli strain, LBG1605, carrying a mutated ptsH gene (encoding HPr (His-containing protein) of the bacterial phosphotransferase system (PTS)) and complemented for PTS activity with the ptsH of Staphylococcus carnosus, exhibited reduced mannitol fermentation activity when transformed with a plasmid bearing this 3574-bp Bs fragment. This fragment contained an incomplete and two complete open reading frames (ORFs). The product of the first complete ORF, a protein composed of 235 amino acids (aa) (25 038 Da), was found to be responsible for the observed reduced mannitol fermentation. The 3′ part of this 705-bp second ORF and the 428-bp incomplete first ORF encode aa sequences exhibiting almost 40% sequence identity. However, the function of these two proteins remains unknown. The third ORF, the 1893-bp prkA gene, encodes a protein (PrkA) of 72 889 Da. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases. Several of the essential aa in the loops known to form the active site of cyclic adenosine 3′,5′-monophosphate (cAMP)-dependent protein kinase appeared to be conserved in PrkA. After expression of prkA and purification of PrkA, we could demonstrate that PrkA can indeed phosphorylate a Bs 60-kDa protein at a Ser residue.

Identification of novel homologues of three low molecular weight subunits of the mitochondrial bc1 complex.

Large-scale random cDNA sequencing projects have been started for several organisms and are a valuable tool for the analysis of quantitative and qualitative aspects of gene expression. However, the reliability of the obtained data is limited as most of the clones are only partially analysed on one strand. As a consequence the sequence entries derived from random cDNA sequencing projects usually comprise incomplete open reading frames. They nevertheless define complete and reliable coding sequences, if two prerequisites are fulfilled: (i) the clones encode very small proteins, and (ii) the clones have a high frequency in the cDNA-banks. The present study describes the use of cDNA databases for the identification of homologues of three low-molecular-weight subunits of the mitochondrial bc1 complex, termed the QCR6, QCR9 and QCR10 proteins. These polypeptides are only characterized for a small number of organisms, have a scarcely defined function and exhibit a low degree of structural conservation if compared between different species. Several clones were identified for each polypeptide by searches with TBLASTN using the known sequences as probes. Most of the database entries contain complete open reading frames and sequencing queries could be excluded due to the abundancy of the clones. Multiple sequence alignments are presented for all three polypeptides and consensus sequences are given which may provide a basis for the investigation of the proteins by site-directed mutagenesis.

Functional cloning of the dihydropteroate synthase gene of Staphylococcus haemolyticus

A 1.7-kilobase fragment of the Staphylococcus haemolyticus chromosome containing the dihydropteroate synthase gene has been cloned by complementation in a temperature-sensitive mutant of Escherichia coli. The gene, designated folP, predicts a gene product of 29613 Da which shares significant amino acid sequence identity with other known bacterial dihydropteroate synthases. Analysis of the DNA sequence upstream and downstream of folP identified two further, incomplete open reading frames, one of which shows predicted amino acid sequence similarity to a second bacterial folic acid synthesis enzyme, dihydroneopterin aldolase.

Sequence and mutational analysis of a tartrate utilization operon from Agrobacterium vitis

The grapevine is the natural host of the tumorigenic bacterium Agrobacterium vitis. Most of the A. vitis isolates can use tartrate, an unusually abundant compound in grapevine. The nopaline strain, AB4, contains a 170-kb conjugative plasmid (pTrAB4) encoding tartrate utilization. A 5.65-kb pTrAB4 region which enables non-tartrate-utilizing Agrobacterium tumefaciens to grow on tartrate was sequenced and mutagenized with the transcriptional fusion transposon Tn5-uidA1. This DNA fragment contains four intact open reading frames (ORFs) (ttuABCD) required for tartrate-dependent growth. The mutant phenotypes of each ORF, their homologies to published sequences, and their induction patterns allowed us to propose a model for tartrate utilization in A. vitis. ttuA encodes a LysR-like transcriptional activator and is transcribed in the absence of tartrate. ttuB codes for a protein with homology to transporter proteins and is required for entry of tartrate into bacteria. ttuC codes for a tartrate dehydrogenase, while ttuD lacks homology to known sequences; the growth properties of ttuD mutants suggest that TtuD catalyzes the second step in tartrate degradation. A fifth incomplete ORF (ttuE) encodes a pyruvate kinase which is induced by tartrate and required for optimal growth. Although the ttuABCD fragment allows growth of A. tumefaciens on tartrate, it does not provide full tartrate utilization in the original A. vitis background.

DNA sequence and transcriptional analysis of the glycoprotein M gene of murine cytomegalovirus

We have characterized the gene encoding the murine cytomegalovirus (MCMV) homologue of the human cytomegalovirus (HCMV) UL100 open reading frame (ORF) that encodes the HCMV glycoprotein M (gM) molecule. It was identified based on its collinearity with MCMV homologues of the HCMV UL99, UL102, UL103 and UL104 ORFs which lie in the HindIII G fragment of the K181 strain of MCMV. Sequencing of a 2.3 kb EcoRI-BamHI subfragment of the EcoRI G fragment adjacent to the EcoRI A fragment revealed the presence of the complete MCMV gM ORF and two incomplete ORFs, which corresponded to homologues of HCMV UL99 and UL102. The MCMV gM ORF consists of 1059 nucleotides and is expressed as a 1.2 kb transcript at late times post-infection. To precisely characterize the gM transcript, the 5' and 3' ends were mapped. It was found that the transcript initiates at nucleotides 740 or 745, and that the site of polyadenylation at nucleotide 1961 occurs downstream of the second potential polyadenylation signal located at nucleotide 1934. Based on these findings the MCMV gM is predicted to consist of 353 residues and when compared with HCMV gM has a 47% level of identity. Of great interest is the finding that the MCMV gM amino acid sequence is completely conserved among six isolates of MCMV that had been shown to exhibit considerable variation both in the MCMV glycoprotein B and the immediate-early 1 gene-encoded pp89 molecule. Thus, this glycoprotein appears to be antigenically conserved.

A non-essential glutamyl aminopeptidase is required for optimal growth of Lactococcus lactis MG1363 in milk

Degenerate PCR primers were designed from the N-terminal amino acid sequence of a glutamyl aminopeptidase (PepA) from Lactococcus lactis. These primers were used to screen a lambda library for clones containing the gene (pepA) encoding PepA. The DNA sequence of a 2.1 kb fragment containing pepA was determined. The sequence revealed the presence of one complete and two incomplete open reading frames (ORFs). The complete ORF encodes a putative protein of 353 amino acids with a predicted N-terminal sequence identical to that determined for purified PepA. The pepA gene was subcloned on an Escherichia coli plasmid vector and production of active PepA was confirmed by means of a zymogram. Mutants of L. lactis in which the pepA gene was inactivated grew to normal cell densities in milk but exhibited a reduced growth rate during the exponential phase. Thus whilst PepA is required for optimal growth it is not essential.

Sequencing and linkage analysis of aCoxiella burnetii 2.1 kbNotI fragment

Most of the Coxiella burnetii isolates (72 of 80) available in our institute share a 2.1 kb NotI fragment. Sequence analysis revealed two incomplete open reading frames (ORF) for putative genes hemA and bcR coding for glutamyl-tRNA-reductase and bicyclomycin resistance protein, respectively. Upon completing the ORF for the hemA gene by sequencing the adjacent NotI/EcoRI fragment a third ORF for the putative prfA gene was determined coding for release factor 1, an enzyme catalysing the last step in protein biosynthesis.

Stringent chemical and thermal regulation of recombinant gene expression by vaccinia virus vectors in mammalian cells.

We developed a stringently regulated expression system for mammalian cells that uses (i) the RNA polymerase, phi 10 promoter, and T phi transcriptional terminator of bacteriophage T7; (ii) the lac repressor, lac operator, rho-independent transcriptional terminators and the gpt gene of Escherichia coli; (iii) the RNA translational enhancer of encephalomyocarditis virus; and (iv) the genetic background of vaccinia virus. In cells infected with the recombinant vaccinia virus, reporter beta-galactosidase synthesis was not detected in the absence of inducer. An induction of at least 10,000- to 20,000-fold occurred upon addition of isopropyl beta-D-thiogalactopyranoside or by temperature elevation from 30 to 37 degrees C using a temperature-sensitive lac repressor. Regulated synthesis of the secreted and highly glycosylated human immunodeficiency virus 1 envelope protein gp120 was also demonstrated. Yields of both proteins were approximately 2 mg per 10(8) cells in 24 hr. Plasmid transfer vectors for cloning and expression of complete or incomplete open reading frames in recombinant vaccinia viruses are described.

A 37.5 kb region of yeast chromosome X includes the SME1, MEF2, GSH1 and CSD3 genes, a TCP-1-related gene, an open reading frame similar to the DAL80 gene, and a tRNA(Arg).

The complete DNA sequence of cosmid clone p59 comprising 37,549 bp derived from chromosome X was determined from an ordered set of subclones. The sequence contains 14 open reading frames (ORFs) containing at least 100 consecutive sense codons. Four of the ORFs represent already known and sequenced yeast genes: B645 is identical to the SME1 gene encoding a protein kinase, required for induction of meiosis in yeast, D819 represents the MEF2 gene probably encoding a second mitochondrial elongation factor-like protein, D678 is identical to the yeast GSH1 gene encoding gamma-glutamylcysteine synthetase and B746 is identical to the CSD3 gene, which plays an as yet unidentified role in chitin biosynthesis and/or its regulation. The deduced amino acid sequence of A550 is 63% identical to the Cc eta subunit of a murine TCP-1-containing chaperonin and more than 35% identical to thermophilic factor 55 from Sulfolobus shibatae, as well as to a number of proteins belonging to the chaperonin TCP-1 family. Open reading frame F551 exhibits homology to two regions of the DAL80 gene located on yeast chromosome XI encoding a pleiotropic negative regulatory protein. In addition, extensive homology was detected in three regions including parts of ORFs A560, B746/CSD3 and the incomplete ORF C852 to three consecutive ORFs of unknown function in the middle of the right arm of chromosome XI. Finally, the sequence contained a tRNA(Arg3) (AGC) gene.