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PubMed2000

Cloning and expression of a novel MAPKK-like protein kinase, lymphokine-activated killer T-cell-originated protein kinase, specifically expressed in the testis and activated lymphoid cells.

A novel protein kinase, TOPK (T-LAK cell-originated protein kinase), was isolated from a lymphokine-activated killer T (T-LAK) cell subtraction cDNA fragment library. The open reading frame of the TOPK gene encodes a protein of 322 amino acids, possessing a protein kinase domain profile. The cap site analysis of the 5'-end of TOPK mRNA revealed two forms, a major full-length form and a minor spliced form at the 5'-site, both encoding the same protein. A BLAST homology search and phylogenetic analysis indicated that TOPK is related to dual specific mitogen-activated protein kinase kinase (MAPKK). The transfection of the TOPK gene to COS-7 cells up-regulated a phosphorylation of p38 MAPK but not ERK1/2 or SAPK/JNK. Gel precipitation study indicated that TOPK protein can be associated with p38 in vitro. Tissue distribution of TOPK mRNA expression was specific for the testis, T-LAK cells, activated lymphoid cells, and lymphoid tumors. On the other hand, deactivated T-LAK cells did not show TOPK mRNA expression. These data suggest that TOPK is a newly identified member of a novel MEK3/6-related MAPKK that may be enrolled in the activation of lymphoid cells and support testicular functions.

Amino Acid Sequence↗

PubMed2002

Analysis of the complete genome of subgroup A' hepatitis B virus isolates from South Africa.

A phylogenetic analysis is presented of six complete and seven pre-S1/S2/S gene sequences of hepatitis B virus (HBV) isolates from South Africa. Five of the full-length sequences and all of the pre-S2/S sequences have been previously reported. Four of the six complete genomes and three of the five incomplete sequences clustered with subgroup A', a unique segment of genotype A of HBV previously identified in 60% of South African isolates using analysis of the pre-S2/S region alone. This separation was also evident when the polymerase open reading frame was analysed, but not on analysis of either the X or pre-core/core genes. Amino acids were identified in the pre-S1 and polymerase regions specific to subgroup A'. In common with genotype D, 10 of 11 genotype A South African isolates had an 11 amino acid deletion in the amino end of the pre-S1 region. This deletion is also found in hepadnaviruses from non-human primates.

Base Sequence↗

PubMed2005

Isolation, sequence analysis, and comparison of two plasmids (28 and 29 kilobases) from the biomining bacterium Leptospirillum ferrooxidans ATCC 49879.

Two plasmids, of 28,878 bp and 28,012 bp, were isolated from Leptospirillum ferrooxidans ATCC 49879. Altogether, a total of 67 open reading frames (ORFs) were identified on both plasmids, of which 32 had predicted products with high homology to proteins of known function, while 11 ORFs had predicted products with homology to previously identified proteins of unknown function. Twenty-four ORFs had products with no homologues in the GenBank/NCBI database. An analysis of the ORFs and other features of the two plasmids, the first to be isolated from a bacterium of the genus Leptospirillum, is presented.

Bacteria↗

PubMed1993

Molecular cloning and nucleotide sequence of a putative trpDC(F)BA operon in Buchnera aphidicola (endosymbiont of the aphid Schizaphis graminum).

A 8,392-nucleotide-long DNA fragment from Buchnera aphidicola (endosymbiont of the aphid Schizaphis graminum) contained five genes of the tryptophan biosynthetic pathway [trpDC(F)BA] which code for enzymes converting anthranilate to tryptophan. These genes are probably arranged as a single transcription unit. Downstream of the trp genes were ORF-V, ORF-VI, and P14, three open reading frames which in Escherichia coli are also found downstream of the trp operon. Upstream of the B. aphidicola trp genes were two unidentified open reading frames, one of which potentially codes for a membrane-spanning protein with a leader sequence. Evidence for the presence of trpB in the endosymbionts of eight additional species of aphids and two species of whiteflies was obtained. These results as well as those of A. E. Douglas and W. A. Prosser (J. Insect Physiol. 38:565-568, 1992) suggest that aphid endosymbionts are capable of synthesizing tryptophan, which is required by the aphid host.

Amino Acid Sequence↗

PubMed1999

Genomic cloning and chromosomal localization of the mouse Mab21l2 locus.

A second mouse gene related to the nematode mab-21 gene has been isolated. This gene, Mab21l2, encodes a transcript with an open reading frame discretely organized in a single exon. It shares 93.3% and 55.5% amino acid identity with the human and worm mab-21 respectively. FISH analysis determined that this gene is on chromosome 3 at a position between bands 3E3 and 3F1. This newly identified mouse gene will be useful in future examination of mab-21 gene function in vertebrate models.

Amino Acid Sequence↗

PubMed2006

An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome.

BACKGROUND: The completed genome sequences of the malaria parasites P. falciparum, P. y. yoelii and P. vivax have revealed some unusual features. P. falciparum contains the most AT rich genome sequenced so far--over 90% in some regions. In comparison, P. y. yoelii is approximately 77% and P. vivax is approximately 55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in Plasmodium has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three Plasmodium species. RESULTS: Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in P. vivax, eight in P. y. yoelii and only six in P. falciparum. Further investigation of the six open reading frames in P. falciparum revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in P. y. yoelii and P. falciparum. One of the P. vivax open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene. CONCLUSION: There is a divergence in the frequencies of mobile genetic elements in the three Plasmodium species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the P. falciparum genome.

Amino Acid Sequence↗

PubMed2002

Results of laparoscopic antireflux procedures in neurologically impaired children.

Although laparoscopic fundoplication is now performed commonly in children, its long-term results in neurologically impaired (NI) children is unknown. We present a single surgeon's experience. During an 8.5 year period, 54 consecutive NI children (age 5 months to 16 years; weight 2.7 to 42 kg) who had failed medical treatment for severe gastroesophageal reflux (GER) underwent laparoscopic Nissen fundoplication without (7) or with (47) gastrostomy. Indications for surgery included failure to thrive and feeding difficulties in all, major vomiting in 42, recurrent chest infections in 44, and inability to take oral medication in 14. Hiatus hernia was present in 14 and delayed gastric emptying in 6 patients. Eight (15%) had undergone previous abdominal surgery. Access was modified according to individual anatomy and 4 or 5 cannulae were used in each patient. Postoperative epidural/morphine analgesia was used in the first 12 to 24 hours, and fluid intake and feeding were started on day 1 and 2, respectively. The average operating time for fundoplication was 2.2 hours (range 1.05 to 3) and for fundoplication and gastrostomy 2.3 hours (range 1.22 to 4.10). Three patients had conversion to open surgery (1 perforated esophagus, 1 hypercarbia and hepatomegaly, 1 camera failure). There were no other operative complications or mortality. One child with Down syndrome developed a food bolus obstruction 3 days postoperatively. The vast majority of patients were discharged home 3 to 4 days following fundoplication and 5 to 7 days following fundoplication and gastrostomy. Postoperative gas bloat was common, diarrhea developed in 4, dumping in 3, and major gastrostomy infection in 1 case. During follow-up (median 5.2, range 3 months to 8.6 years), 9 (16%) children showed signs of persistent/recurrent problems. Investigations showed a recurrent hiatus hernia in 1 (requiring re-operation) and minor reflux in 3 patients. To date 6 (11%) children have died of their background conditions. In NI children, laparoscopic fundoplication is safe and successful. Awareness of the differences in access and risks for NI and normal children is important. Compared with historical data for open technique, laparoscopic fundoplication produces lower mortality and morbidity and similar intermediate and long-term results.

Adolescent↗

PubMed1996

Sequence analysis of the 43 kb CRM1-YLM9-PET54-DIE2-SMI1-PHO81-YHB4-PFK1 region from the right arm of Saccharomyces cerevisiae chromosome VII.

The nucleotide sequence of a 43 118 bp fragment from chromosome VII of Saccharomyces cerevisiae has been determined and analysed. The fragment originates from the right arm of chromosome VII. It starts approximately 11 kb centromere-proximal to the per54 marker and ends in the middle of the PFK1 gene. The sequence contains a small nuclear RNA gene (SNR7) and 29 open reading frames (ORFs) larger than 100 amino acids. Six of these were completely internal to or partially overlapped other ORFs. Six previously described genes, YLM9/MRPL9, CRM1, DIE2, SMI1, PHO81 and YHB4, were mapped to this region in addition to pet54 and PFK1. Of the remaining 17 ORFs, four showed homology with other S. cerevisiae genes and four, including one of the partially overlapping ORFs, with genes from other organisms. Eight ORFs had no homology with any sequence in the databases.

Base Sequence↗

PubMed1997

Sequence analysis of Candida albicans phosphoribosyl-aminoimidazole carboxylase (ADE2) gene.

The nucleotide sequence of the Candida albicans ADE2 gene, which encodes phosphoribosylaminoimidazole carboxylase, has been determined. The sequence possesses an uninterrupted open reading frame of 1704 nucleotides corresponding to 568 amino acid residues. The deduced amino acid sequence shares a high degree of homology with ADE2 homologues in other fungal species including Saccharomyces cerevisiae, Pichia methanolica, Schwanniomyces occidentalis and Schizosaccharomyces pombe. Three regions of amino acid sequence were highly conserved among all reported ADE2 genes. The hexanucleotide TGACTC characteristic of genes involved in purine and amino acid biosynthesis is located in front of putative TATA boxes in the promoter region.

Amino Acid Sequence↗

PubMed1995

A gene proposed to encode a transmembrane domain of an ABC transporter is expressed in wheat mitochondria.

In a study of transcribed regions of the wheat mitochondrial genome, we identified an open reading frame of 720 bp, which was consequently designated orf240. The amino acid sequence deduced from orf240 shows a high level of similarity with HelC, a protein essential for c-type cytochrome biogenesis in the photosynthetic purple bacterium Rhodobacter capsulatus. HelC is part of a putative heme ABC transporter. An open reading frame homologous to orf240 is present in the mitochondrial genome of Marchantia polymorpha. The wheat gene is expressed as an mRNA of 2.8 kb, which is further processed to smaller transcripts. The transcript is highly edited, with 36 C to U modifications found in the coding region of all cDNAs sequenced. RNA editing is responsible for changes in 14% of the amino acids specified by the transcript.

ATP-Binding Cassette Transporters↗

PubMed1991

Pea chloroplast genes encoding a 4 kDa polypeptide of photosystem I and a putative enzyme of C1 metabolism.

The nucleotide sequence of 3.2 kbp of pea chloroplast DNA located upstream from the petA gene for cytochrome f, and previously reported to contain the gene for a photosystem I polypeptide, has been determined. Three open reading frames of 587, 40 and 157 codons have been identified. Orf40 encodes a highly conserved, hydrophobic, membrane-spanning polypeptide, and is identified as the gene psaI for the 4 kDa subunit of photosystem I. Orf587 is an extended version of the gene zfpA previously identified as encoding a conserved putative zinc-finger protein. The product of orf587 shows extensive homology to an unidentified open reading frame cotranscribed with a gene for folate metabolism in Escherichia coli and local homology to a region of the beta subunit of rat mitochondrial propionyl-CoA carboxylase. It is suggested that the product of orf587 is an enzyme of C1 metabolism and is unlikely to be a regulatory DNA-binding protein. Orf157 potentially encodes an unidentified basic protein, but the protein sequence is not conserved in other plants.

Amino Acid Sequence↗

PubMed1992

The 3'-nucleotide sequence of an ordinary strain of potato virus S.

The sequence of 1346 nucleotides of the 3'-terminal region of an ordinary strain of potato virus S was determined from cloned cDNA. This portion of the viral RNA contains two major open reading frames (ORFs), encoding the coat protein of M(r)33K and a protein of M(r)11K 3' to the coat protein, both of which showed high homology, 93% and 79%, respectively, with the equivalent proteins of the Andean strain. A major block of amino acids that differ between the ordinary and Andean strains was present in both the coat protein and the 11K. These blocks may be responsible for the substantial differences between the ordinary and Andean strains at the symptom and aphid transmissibility levels.

Amino Acid Sequence↗

PubMed1994

Mapping of Marek's disease virus genome: identification of junction sequences between unique and inverted repeat regions.

Polymerase chain reaction (PCR) to amplify MDV DNA and subsequent sequencing identified the junction of TRL/UL, UL/IRL, IRS/US, and US/TRS. The TRL/UL junction is located 192 bp downstream of the last EcoRI site in the TRL region, while the UL/IRL junction is located 192 bp upstream of the first EcoRI restriction enzyme site in the IRL region. The IRS/US junction is located 950 bp downstream of the second EcoRI site in the IRS region, while the US/TRS junction is located 950 bp upstream of the first EcoRI restriction enzyme site in the TRS region. BamHI restriction enzyme mapping of one of the PCR products identified two novel DNA subfragments, BamHI-U2 and -P4, upstream of the US/TRS junction of the MDV genome. Sequencing of the BamHI-D fragment revealed a novel open reading frame (ORF) encoding a 155 amino acid protein. The TRL/UL junction is located in this ORF. The N-terminal 65 amino acids of this protein is homologous to the N-terminal region of the previously reported pp38, which is located in the UL/IRL region. Computer-assisted analysis indicated that both are transmembrane proteins and that they share an antigenic domain.

Amino Acid Sequence↗

PubMed1997

Unidentified open reading frames in the genome of Methanococcus jannaschii are similar in sequence to an archaebacterial gene for tRNA nucleotidyltransferase.

The protein sequence of ATP/CTP:tRNA nucleotidyltransferase (cca) from Sulfolobus shibatae was used to search open reading frames in the genome of Methanococcus jannaschii. Translations of two unidentified open reading frames showed significant sequence similarity to portions of the Sulfolobus cca protein. When the two open reading frames were joined together, the expanded open reading frame was similar in sequence to the entire Sulfolobus cca protein and displayed features of the active site signature sequence proposed for members of class I enzymes within the superfamily of nucleotidyltransferases (Yue et al., 1996, RNA 2, 895-908). A possible UUG start codon was identified based on significant sequence similarity of the resulting amino-terminal region to that of Sulfolobus, and on a six-base complementarity between an adjacent upstream sequence and Methanococcus 16S rRNA.

Amino Acid Sequence↗

PubMed2005

Genetic organization of a plasmid from an industrial wastewater bioreactor.

Pseudomonas strain CT14 was isolated from activated sludge. Strain CT14 contained a 55, 216 bp plasmid that was characterized by sequence analysis. The plasmid had a modular structure with 51 open reading frames (ORFs) that were distributed between two clearly demarcated domains. Domain I primarily contained genes for plasmid-related functions and a novel origin of replication. Domain II bore evidence of extensive transposition and recombination. Domain II contained several genes from a meta-cleavage pathway for aromatic rings. These genes appeared to have been recruited from different hosts. This observation suggests that sequencing pCT14 may have revealed an intermediate stage in the evolution of a new assemblage of meta-cleavage pathway genes.

Base Sequence↗

PubMed1992

The UDP-N-acetylglucosamine 1-carboxyvinyl-transferase of Enterobacter cloacae. Molecular cloning, sequencing of the gene and overexpression of the enzyme.

The UDP-N-acetylglucosamine 1-carboxyvinyltransferase (enolpyruvyltransferase, EC 2.5.1.7) which catalyses the first committed step in the biosynthesis of the bacterial cell-wall peptidoglycan was purified to near homogeneity from Enterobacter cloacae and the NH2-terminal amino-acid sequence determined. Using the polymerase chain reaction a 53-bp DNA fragment was synthesized; this fragment encodes the NH2-terminal sequence of the enzyme. A clone was then isolated which contained an open reading frame of 1257 bp coding for a protein of 419 amino acids. This protein was overexpressed 100-fold in transformed Escherichia coli cells and shown to possess the enolpyruvyltransferase activity. The overall amino-acid sequence of the enolpyruvyltransferase is significantly similar to that of the 5-enolpyruvylshikimate 3-phosphate synthase, the only other enzyme known to catalyse the transfer of the enolpyruvate moiety of phosphoenolpyruvate to a substrate.

Alkyl and Aryl Transferases↗

PubMed1994

Abundant expression of thromboxane synthase in rat macrophages.

The cloned cDNA for rat thromboxane (TX) synthase with a size of 1851 bp contained a 1599-bp open reading frame which encoded a 533-amino acid protein sharing 79.7% identity with human TX synthase. RNA blot analysis was carried out with rat cells and tissues. Rat peritoneal macrophages most abundantly expressed mRNA for TX synthase, and its level was not changed by in vivo stimulation of casein. Bone marrow, spleen, lung and thymus also expressed the TX synthase gene. These findings suggest the possibility that TXA2 plays a role in the immune system.

Amino Acid Sequence↗

PubMed2002

Identification of the novel proteins Yip4p and Yip5p as Rab GTPase interacting factors.

The Rab GTPases are key regulators of membrane traffic. Yip1p is a membrane protein of unknown function that has been reported to interact with the Rabs Ypt1p and Ypt31p. In this study we identify Yif1p, and two unknown open reading frames, Ygl198p and Ygl161p, which we term Yip4p and Yip5p, as Yip1p-related sequences. We demonstrate that the Yip1p-related proteins possess several features: (i) they have a common overall domain topology, (ii) they are capable of biochemical interaction with a variety of Rab proteins in a manner dependent on C-terminal prenylation, and (iii) they share an ability to physically associate with other members of the YIP1 family.

Adaptor Proteins, Signal Transducing↗