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Observation of positive selection within hypervariable regions of a newly identified DNA virus (SEN virus)(1).

To elucidate the evolution of SEN virus (SEN-V), serial sequences of chronically SEN-V-infected patients were analyzed. In the hypervariable regions, non-synonymous substitutions significantly predominated. This could be attributed to positive selection in evading immune surveillance of the hosts and to establish a persistent infection. On the basis of the sequences in the two open reading frames of SEN-V DNA, the rate of synonymous substitutions was 7.32 x 10(-4) per site per year. Since this rate is close to RNA viruses and higher than other DNA viruses, the SEN-V might be replicated by machinery with poor or no proofreading function.

Chronic Disease↗

Molecular cloning of cDNA encoding porcine interleukin-15.

Interleukin-15 (IL-15) is a recently identified growth and differentiation factor with an important potential role in the initial immune responses to infection. To enable the study of the role of this cytokine in the protective immune-mechanisms generated against parasitic diseases of swine, cDNA was generated from a macrophage enriched adherent cell population from peripheral blood mononuclear cells (PBMC). This cDNA was used for the enzymatic amplification of the porcine IL-15 sequence using human IL-15-derived primers. The open-reading frame of the porcine IL-15 cDNA is 486 base pairs (bp) in length and encodes a 162-amino-acid (aa) protein. Comparisons of the predicted swine protein sequence with those predicted from human, bovine and mouse IL-15 sequences indicate similarities of 82.1, 84.6, and 71.6%, respectively.

Amino Acid Sequence↗

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.

Amino Acid Sequence↗

The Hansenula polymorpha (strain CBS4732) genome sequencing and analysis.

The methylotrophic yeast Hansenula polymorpha is a recognised model system for investigation of peroxisomal function, special metabolic pathways like methanol metabolism, of nitrate assimilation or thermostability. Strain RB11, an odc1 derivative of the particular H. polymorpha isolate CBS4732 (synonymous to ATCC34438, NRRL-Y-5445, CCY38-22-2) has been developed as a platform for heterologous gene expression. The scientific and industrial significance of this organism is now being met by the characterisation of its entire genome. The H. polymorpha RB11 genome consists of approximately 9.5 Mb and is organised as six chromosomes ranging in size from 0.9 to 2.2 Mb. Over 90% of the genome was sequenced with concomitant high accuracy and assembled into 48 contigs organised on eight scaffolds (supercontigs). After manual annotation 4767 out of 5933 open reading frames (ORFs) with significant homologies to a non-redundant protein database were predicted. The remaining 1166 ORFs showed no significant similarity to known proteins. The number of ORFs is comparable to that of other sequenced budding yeasts of similar genome size.

Base Sequence↗

Sequence characterization of the matrix protein genes of parainfluenza virus types 4A and 4B.

The complete nucleotide sequences of the matrix protein (M) genes of parainfluenza virus types 4A and 4B (PIV-4A and -4B) were determined from cDNA of the mRNA, and found to be 1548 bases in length, exclusive of poly(A) sequences. The sequences contained a large open reading frame of 1146 nucleotides encoding 362 amino acids. A high degree of identity (96.1%) was observed between the amino acid sequences of PIV-4A and PIV-4B M. These M sequences were compared with those of 10 other paramyxoviruses and a phylogenetic tree was constructed.

Amino Acid Sequence↗

Cloning and nucleotide sequence of a gene upstream of the eaeA gene of enterohemorrhagic Escherichia coli O157:H7.

A DNA segment located immediately upstream of the eaeA gene of enterohemorrhagic Escherichia coli O157:H7 strain HA1 was cloned and sequenced. This segment contained an open reading frame encoding a predicted protein of 156 amino acids. A database search identified similar open reading frames upstream of the eaeA gene in two other bacterial pathogens, i.e. enteropathogenic E. coli and Citrobacter freundii. The predicted amino acid sequence of the enterohemorrhagic E. coli protein shared 96.8% and 94.2% identity with the enteropathogenic E. coli and C. freundii sequences, respectively. Because the open reading frame is located within the locus of enterocyte effacement region of the E. coli chromosome, a 'hot spot' for insertion of virulence factor genes, and shares high sequence homology with attaching and effacing EPEC and C. freundii, this protein may be associated with pathogenicity of E. coli O157:H7.

Amino Acid Sequence↗

Bacteroides fragilis transfer factor Tn5520: the smallest bacterial mobilizable transposon containing single integrase and mobilization genes that function in Escherichia coli.

Many bacterial genera, including Bacteroides spp., harbor mobilizable transposons, a class of transfer factors that carry genes for conjugal DNA transfer and, in some cases, antibiotic resistance. Mobilizable transposons are capable of inserting into and mobilizing other, nontransferable plasmids and are implicated in the dissemination of antibiotic resistance. This paper presents the isolation and characterization of Tn5520, a new mobilizable transposon from Bacteroides fragilis LV23. At 4,692 bp, it is the smallest mobilizable transposon reported from any bacterial genus. Tn5520 was captured from B. fragilis LV23 by using the transfer-deficient shuttle vector pGAT400DeltaBglII. The termini of Tn5520 contain a 22-bp imperfect inverted repeat, and transposition does not result in a target site repeat. Tn5520 also demonstrates insertion site sequence preferences characterized by A-T-rich nucleotide sequences. Tn5520 has been sequenced in its entirety, and two large open reading frames whose predicted protein products exhibit strong sequence similarity to recombinase-integrase enzymes and mobilization proteins, respectively, have been identified. The transfer, mobilization, and transposition properties of Tn5520 have been studied, revealing that Tn5520 mobilizes plasmids in both B. fragilis and Escherichia coli at high frequency and also transposes in E. coli.

Bacteroides fragilis↗

Expression of the two nested overlapping reading frames of turnip yellow mosaic virus RNA is enhanced by a 5' cap and by 5' and 3' viral sequences.

The translation efficiency of an mRNA molecule is typically determined by its 5'- and/or 3'-untranslated regions (UTRs). Previously, we have found that the 3'-UTR of Turnip yellow mosaic virus (TYMV) RNA enhances translation synergistically with a 5' cap. Here, we use a luciferase reporter system in cowpea protoplasts to show that the 5' 217 nucleotides from TYMV genomic RNA enhance expression relative to a vector-derived 17-nucleotide 5'-UTR. Maximum expression was observed from RNAs with a cap and both 5' and 3' TYMV sequences. In paired reporter constructs, the 5' 217 nucleotides harboring the UTR and the first 43 or 41 codons of the two overlapping TYMV open reading frames (ORFs), ORF-69 and ORF-206, respectively, were fused in frame with the luciferase gene. This allowed expression from the initiation codon of each ORF (AUG69 and AUG206) to be monitored separately but from the normal sequence environment. Expression from both AUG codons was heavily dependent on a 5' cap, with a threefold-higher expression occurring from AUG69 than from AUG206 in the presence of the genomic 3'-UTR. Changes that interrupted the cap/3'-UTR synergy (i.e., removal of the cap or TYMV 3'-UTR) resulted in a higher proportion of initiation from AUG206. Mutation of the 3'-UTR to prevent aminoacylation, as well as deletion of 75% of the 5'-UTR, likewise resulted in a lower ratio of expression from AUG69 relative to AUG206. Mutation of each AUG initiation codon increased initiation from the other. Taken together, these results do not fully conform to the expectations of standard leaky ribosomal scanning and leave open the precise mechanism of ribosome commitment to AUG69 and AUG206. However, our observations do not support a recent proposal based on in vitro studies in which the 3'-UTR is proposed to direct cap-independent initiation specifically at AUG206 and not at AUG69 (S. Barends et al., Cell 112:123-129, 2003).

3' Untranslated Regions↗

A host-vector system for a cellulose-producing Acetobacter strain.

An indigenous plasmid, named pAH4, was detected in a cellulose-producing Acetobacter strain. This plasmid, consisting of 4002 bp, contained an AT-rich region and encoded several open reading frames, as deduced by the complete nucleotide sequence. One of the putative open reading frames showed homology with replication proteins of other plasmids. A shuttle vector of Escherichia coli and this strain was constructed by connecting pAH4 to pUC18. Electroporation of the shuttle vector into the strain yielded 1.7 x 10(5) ampicillin resistant transformants per microgram DNA. The shuttle plasmid was very stably maintained in the strain.

Acetobacter↗

[Molecular cloning of a protein antigen gene of Cysticercus cellulosae].

OBJECTIVE: To immunoscreen one protein antigen gene from a cDNA library of Cysticercus cellulosae. METHODS: A eDNA library of C. cellulosae was constructed after cDNA was synthesized, and immunoscreened using rabbit anti-C. cellulosae polyclone antibody. The gene structure and its possible function were analyzed by comparing with the sequences available in the GenBank, after the insert of positive clone was subcloned to pBluescript SK plasmid and the nucleotide sequence of the cDNA was determined by dideoxynucleotide chain termination method using a Taq DyeDeoxy Terminator Cycle Sequencing Kit. The amino acid sequence was deduced from nucleotide sequence using GENETYX software. Homological search of the nucleotide sequences was done using BLAST in GenBank. RESULTS AND CONCLUSION: A cDNA clone of 1320 bp was isolated. The clone contained one open reading frame composed of 1260 bp encoding 420 amino acids, in which two potential glycosylation sites were found. The partial nucleotide sequence of the gene fragment showed high homology with the essential spectrin gene of Caenorhabditis elegans and the erythrocyte surface antigen gene of Plasmodium falciparum, when the gene fragment was homologically analyzed in GenBank.

Amino Acid Sequence↗

[Cloning and characterization of a novel mouse aging-related gene Arzc].

OBJECTIVE: To clone and identify novel mouse aging-related genes. METHODS: The improved differential display reverse transcription-polymerase chain reaction method was used to analyze the differential expression of old and young BALB/C mouse cortex tissues. The novel expression sequence targets (EST) with differential expression were further confirmed by Northern blot and used as original sequence to clone the full-length cDNA sequence by bioinformatics technique. The reverse transcription products of BALB/C mouse cortex total RNA was used as the amplification template. RESULTS: A total of 42 differentially expressed EST were obtained. Homologic analysis showed that 29 EST represented known cDNAs and 13 were probably new EST. One of the EST, which were confirmed to have down regulative expression in the old mouse cortex tissues by Northern blot analysis, was used to obtain the full-length cDNA sequences from reverse transcription products of total RNA of BALB/C mice cortex by bioinformation method. A 1 382 bp of cDNA sequence including the EST was obtained and designed as Arzc (GenBank accession number: AY344585). The Arzc cDNA contains an open reading frame of 261 bp and encodes a peptide of 86 amino acids residuals. FASTA analysis showed that the deduced peptide had a homology with a portion of integrase/recombinase, a member of a phage integrase family. CONCLUSION: A novel mouse gene that is probably related to aging was identified and cloned.

Aging↗

Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3.

The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http:@www.nite.go.jp.

Chromosomes, Archaeal↗

Cryptic open reading frames in plasmid vector backbone sequences can provide highly immunogenic cytotoxic T-lymphocyte epitopes.

Murine tumor cells obtained through transfection of expression plasmids carrying activated cellular and/or viral oncogenes constitute formidable tools for immunological tumor research. As reported previously, mouse embryo cells of C57BL/6 origin, transformed by mutated p53 or human papilloma virus type 16 (HPV16), present, at their surface, MHC-bound peptides that are derived from the p53 and the HPV16 E7 oncoproteins, respectively, which can serve as a target for a highly effective antitumor T-cell response. Here, we describe the identification, through molecular cloning, of an additional, highly immunodominant peptide that is presented by the aforementioned HPV16- and p53-transformed cells. This peptide is encoded by a cryptic open reading frame in the backbone sequences of the plasmids that had been used to generate these cells. Considerable amounts of transcripts encompassing this open reading frame were detected in the cells concerned. These transcripts were the result of the bidirectional nature of the retroviral long terminal repeat (LTR) present in the expression plasmids used for transfection, which resulted in transcription of the gene of interest, as well as in transcription of the vector sequences positioned at the other side of the LTR. Due to this mechanism, all tumor cells harboring LTR-driven expression plasmids expressed the highly immunogenic peptide, whereas cells containing plasmids driven by more unidirectional promoters exhibited lower levels of this peptide. LTR-driven expression plasmids were also shown to encode this peptide epitope when used for DNA vaccination, as mice vaccinated with such a plasmid developed a CTL response against this peptide. Our data show that awareness of plasmid backbone-derived epitopes is of crucial importance for the correct interpretation of preclinical experiments and for the design of DNA vaccines.

Amino Acid Sequence↗

Banana bract mosaic virus: characterisation using potyvirus specific degenerate PCR primers.

Banana bract mosaic (BBMV) is a relatively new, non-persistently aphid transmitted disease of bananas in the Philippines. Partially purified preparations from infected plants contained low numbers of flexuous virions, 660 to 760 nm in length, and a 38kDa protein, possibly the coat protein, which reacted with a general potyvirus antiserum in western blots. There were insufficient virions for conventional antiserum production or cDNA synthesis. Therefore, DNA was amplified using potyvirus-specific degenerate primers and reverse transcriptase PCR. The PCR products were cloned, sequenced and analysed and contained a 5' open reading frame of up to 150 amino acids and a 3' untranslated region of up to 190 nucleotides which were clearly related to the C-terminal half of the coat proteins and the 3' untranslated regions, respectively of potyviruses. The BBMV open reading frame amino acid sequence was most similar to the C-terminal half of the maize dwarf mosaic potyvirus coat protein (71.3% similarity) and the BBMV 3' untranslated region was most similar to that of ornithogalum mosaic potyvirus (39.6% similarity). Our results show that BBMV is a distinct potyvirus and also demonstrate the application of virus group specific primers in the characterisation of previously undescribed viruses.

Amino Acid Sequence↗

Trans activation of the Escherichia coli ato structural genes by a regulatory protein from Bacillus megaterium: potential use in polyhydroxyalkanoate production.

A Bacillus megaterium genomic fragment, which encoded an activator homologous to sigma 54 regulators and which was capable of activating Escherichia coli ato genes in trans, was detected in a gene library of B. megaterium screened for beta-ketothiolase activity. The fragment presented only one complete open reading frame (ORF1), which encoded a protein of 398 amino acids. The recombinant plasmid complemented mutations in the Escherichia coli atoC regulatory gene. The constitutive expression of the E. coli ato operon mediated by ORF1 could be useful for the synthesis of polyhydroxyalkanoates with different flexibility properties by recombinant E. coli strains.

Amino Acid Sequence↗

The cDNA cloning and mRNA expression of rat protein C.

We cloned a cDNA coding for rat protein C, which provides hybridization probes for the detection of protein C mRNA in several tissues. The cloned cDNA was 1543 bp long and contained a single open reading frame of 1383 nucleotides. The proposed rat protein C precursor contained 461 amino acid residues: a 41 amino acid preproleader sequence, and light (155 amino acids) and heavy (263 amino acids) chains joined by a Lys-Arg dipeptide. Northern blot analysis showed that the rat protein C mRNA was expressed not only in the liver, but also in the kidney.

Amino Acid Sequence↗

Cloning and sequence analysis of a full length cDNA encoding human mitochondrial 3-oxoacyl-CoA thiolase.

The cDNA sequence of human mitochondrial 3-oxoacyl-CoA thiolase was determined. The nucleotide sequence contains an open reading frame of 1191 base pairs and encodes an amino acid sequence of 397 residues which exhibits 86.6% homology with that of the rat enzyme. Northern blot analysis gave a single mRNA species of 1.6 kb in the human liver, fibroblasts and intercostal muscle.

Acetyl-CoA C-Acyltransferase↗

Cloning and sequencing of two new fli genes, the products of which are essential for Salmonella flagellar biosynthesis.

We have identified two new open reading frames downstream from fliC, which appear to encode 19- and 20-kDa proteins that are essential for flagellar formation. The nucleotide and the predicted amino acid sequences of the genes are presented. Both genes, termed fliU and fliV, are preceded by the flagellar-specific -10 consensus promoter DNA sequence, suggesting their expression in the earlier stages of flagellar-component biosynthesis.

Amino Acid Sequence↗