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PubMed2005

The Shiga toxin 1-converting bacteriophage BP-4795 encodes an NleA-like type III effector protein.

In this study, the complete DNA sequence of Shiga toxin 1-converting bacteriophage BP-4795 was determined. The genome of BP-4795 consists of 85 open reading frames, including two complete IS629 elements and three morons at the end of its late regulatory region. One of these morons encodes a type III effector that is translocated by the locus of enterocyte effacement-encoded type III secretion system into HeLa cells, where it localizes with the Golgi apparatus.

Base Sequence↗

PubMed1997

Molecular cloning and characterization of a cDNA encoding putative phospholipid hydroperoxide glutathione peroxidase from spinach.

A cDNA encoding spinach putative phospholipid hydroperoxide glutathione peroxidase (PHGPX) was cloned and sequenced. The cDNA included an open reading frame that encoded a polypeptide of 171 amino acid residues. The deduced amino acid sequence showed about 77 and 50% similarity to plant putative PHGPXs and mammalian PHGPXs, respectively. PCR product with the same size as that of the spinach putative PHGPX were obtained from maize, soybeans, and Arabidopsis, suggesting the expression of putative PHGPX genes in other plants.

Amino Acid Sequence↗

PubMed2006

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.

The S. cerevisiae genome is the most well-characterized eukaryotic genome and one of the simplest in terms of identifying open reading frames (ORFs), yet its primary annotation has been updated continually in the decade since its initial release in 1996 (Goffeau et al., 1996). The Saccharomyces Genome Database (SGD; www.yeastgenome.org) (Hirschman et al., 2006), the community-designated repository for this reference genome, strives to ensure that the S. cerevisiae annotation is as accurate and useful as possible. At SGD, the S. cerevisiae genome sequence and annotation are treated as a working hypothesis, which must be repeatedly tested and refined. In this paper, in celebration of the tenth anniversary of the completion of the S. cerevisiae genome sequence, we discuss the ways in which the S. cerevisiae sequence and annotation have changed, consider the multiple sources of experimental and comparative data on which these changes are based, and describe our methods for evaluating, incorporating and documenting these new data.

Base Sequence↗

PubMed2002

3-Hydroxykynurenine transaminase identity with alanine glyoxylate transaminase. A probable detoxification protein in Aedes aegypti.

This study describes the functional characterization of a specific mosquito transaminase responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). The enzyme was purified from Aedes aegypti larvae by ammonium sulfate fractionation, heat treatment, and various chromatographic techniques, plus non-denaturing electrophoresis. The purified transaminase has a relative molecular mass of 42,500 by SDS-PAGE. N-terminal and internal sequencing of the purified protein and its tryptic fragments resolved a partial N-terminal sequence of 19 amino acid residues and 3 partial internal peptide sequences with 7, 10, and 7 amino acid residues. Using degenerate primers based on the partial internal sequences for PCR amplification and cDNA library screening, a full-length cDNA clone with a 1,167-bp open reading frame was isolated. Its deduced amino acid sequence consists of 389 amino acid residues with a predicted molecular mass of 43,239 and shares 45-46% sequence identity with mammalian alanine glyoxylate transaminases. Northern analysis shows the active transcription of the enzyme in larvae and developing eggs. Substrate specificity analysis of this mosquito transaminase demonstrates that the enzyme is active with 3-HK, kynurenine, or alanine substrates. The enzyme has greater affinity and catalytic efficiency for 3-HK than for kynurenine and alanine. The biochemical characteristics of the enzyme in conjunction with the profiles of 3-HK transaminase activity and XA accumulation during mosquito development clearly point out its physiological function in the 3-HK to XA pathway. Our data suggest that the mosquito transaminase was evolved in a manner precisely reflecting the physiological requirement of detoxifying 3-HK produced in the tryptophan oxidation pathway in the mosquito.

Aedes↗

PubMed2001

Molecular characterization of HIV type 1 vpu genes from mothers and infants after perinatal transmission.

We compared 162 vpu sequences of human immunodeficiency virus type 1 (HIV-1) in peripheral blood mononuclear cell DNA of 6 infected mother-infant pairs after perinatal transmission, and found a 90.12% frequency of intact vpu open reading frames. The heterogeneity of vpu genes between epidemiologically linked mother-infant pairs was lower compared with epidemiologically unlinked individuals. However, the variability of vpu genes was higher than that seen for other HIV-1 genes, including vif, vpr, tat, and gag p17 from the same mother-infant pairs. Moreover, the infants' sequences displayed patterns similar to those seen in their mothers. The functional domains essential for Vpu activity, including efficient release of virus particles from infected cells and CD4 degradation, were conserved in most of the sequences. In a phylogenetic analysis, the 162 sequences from 6 mother-infant pairs formed distinct clusters for each mother-infant pair sequences and grouped with subtype B sequences. These data support the importance of vpu in HIV-1 replication of mother-infant isolates that are involved in perinatal transmission.

Adult↗

PubMed2000

A vestigial X open reading frame in duck hepatitis B virus.

Duck hepatitis B virus (DHBV) appears to lack a homologue of the X protein found in mammalian hepadnaviruses. By replacing stop codons in the corresponding region of the DHBV genome, a hypothetical protein which closely matches the hydrophilicity profile of X proteins can be predicted, despite limited sequence homology. We conclude that a full-length X protein was once a common feature of the hepadnaviruses, conserved in structure but not sequence.

Amino Acid Sequence↗

PubMed1994

Isolation and characterization of the LEU2 gene of Hansenula polymorpha.

A DNA fragment carrying the LEU2 gene of methylotrophic yeast Hansenula polymorpha was isolated by complementation of the leuB mutation of Escherichia coli. The nucleotide sequence of the isolated DNA fragment contains an open reading frame of 363 codons, coding for a protein 80% identical to the LEU2 gene product of Saccharomyces cerevisiae. Further downstream, there is a partial reading frame with no obvious similarity to known proteins. The LEU2 gene of H. polymorpha cannot complement the leu2 mutation of S. cerevisiae.

3-Isopropylmalate Dehydrogenase↗

PubMed1991

Identification and organization of carbon dioxide fixation genes in Xanthobacter flavus H4-14.

The genes encoding the large (cfxL) and small (cfxS) subunits of ribulose-1,5-bisphosphate carboxylase (RuBisC/O) from Xanthobacter flavus H4-14 were identified and characterized. The RuBisC/O genes are separated by 11 bp and cotranscribed in Escherichia coli from the lac promoter in the order cfxLS. Primer extension and R-loop experiments with RNA isolated from autotrophically grown X. flavus H4-14 showed that transcription of cfxL and cfxS initiated 22 bp upstream from cfxL and resulted in a mRNA of at least 2.3 kb. DNA sequence analysis identified the start of an open reading frame transcribed divergently from cfxL, and displaying significant similarities with genes belonging to the lysR family of transcriptional activators. Downstream from cfxS an additional open reading frame was identified with unknown function. Expression studies showed that the genes encoding fructosebisphosphatase (cfxF) and phosphoribulokinase (cfxP) are located downstream from cfxLS. The cfxF and cfxP genes are cotranscribed in the same direction as cfxLS in the order cfxFP.

Amino Acid Sequence↗

PubMed1991

Linear DNA plasmids of the perennial ryegrass choke pathogen, Epichloë typhina (Clavicipitaceae).

Epichloë typhina is a clavicipitaceous ascomycete which systemically infects grasses, causes choke disease of host inflorescences, and is related to a group of mutualistic grass endophytes. Three plasmids of 7.5, 2.1 and 2.0 kilobase pairs were found in mitochondrial DNA preparations of an E. typhina isolate from perennial ryegrass (Lolium perenne). Results of nuclease digestion indicated that the plasmids, designated Et7.5L, Et2.1L, and Et2.0L, were linear, double-stranded DNAs with protein linked to their 5'-ends (plDNA). The plasmids shared little or no homology with each other, and were not integrated into the mitochondrial or nuclear genomes. No homologous plasmids were detected in isolates of E. typhina from other grass hosts, anamorphic endophytes, or other Clavicipitaceae. However, other plasmids were present in Balansia obtecta and Claviceps purpurea. A partial sequence of one of the E. typhina plasmids, Et2.0L, indicated an open reading frame when UGA was assumed to encode tryptophan. The inferred amino acid sequence had 24% identity over 258 amino acids in two regions of the reverse transcriptase encoded by the circular Mauriceville and Varkud plasmids of Neurospora spp. The homologies included six segments conserved in RNA template-dependent DNA or RNA polymerases.

Amino Acid Sequence↗

PubMed1993

Isolation and structure of an acetolactate synthase gene from Schizosaccharomyces pombe and complementation of the ilv2 mutation in Saccharomyces cerevisiae.

A gene encoding a functional acetolactate synthase (ALS) subunit has been isolated from the fission yeast Schizosaccharomyces pombe, and has been structurally and genetically characterized. The approximate 5-kbp cloned DNA segment was found to contain a 2007-bp open reading frame capable of encoding a 669 aminoacid polypeptide which exhibited 57.1% similarity to the corresponding ALS subunit from Saccharomyces cerevisiae. The putative ilv1 isolated from S. pombe was shown to encode a functional subunit of acetolactate synthase by complementation of an S. cerevisiae strain deleted for the ILV2 locus.

Acetolactate Synthase↗

PubMed1991

Expression of rotavirus proteins encoded by alternative open reading frames of genome segment 11.

The nucleotide sequence of rotavirus genome segment 11 shows that this gene contains three potential open reading frames. We used several approaches to determine whether any polypeptides other than NS26, the primary protein product, are expressed. In particular, we sought to determine whether the strong out-of-phase start codon present at nucleotides 80-82, which would encode a protein of 92 amino acids, is used in vivo or in cell-free systems. Several modifications of gene 11 were made and found to produce proteins from the different initiation codons in cell-free transcription-translation systems. The protein from the out-of-phase open reading frame was shown to be expressed in rotavirus-infected MA104 cells; this was demonstrated using monospecific sera prepared to this protein expressed in Spodoptera frugiperda insect cells infected with a baculovirus recombinant containing only the out-of-phase open reading frame. The origin of some of the lower-molecular-weight bands serologically related to the primary product of gene 11, NS26, was also studied by selective immunoprecipitation using two different sera made from recombinant baculovirus lysates. All of these polypeptides are present in infected cells in a complex which is still incompletely defined.

Amino Acid Sequence↗

PubMed1992

The complete nucleotide sequence of the JS strain of human parainfluenza virus type 3: comparison with the Wash/47885/57 prototype strain.

The nucleotide sequence of the JS strain of human parainfluenza virus type 3 (PIV3) was determined from a series of 14 overlapping cDNA clones and was compared to that of the previously sequenced prototype PIV3 strain, Wash/47885/57 (Galinski, 1991). Overall, there were 630 (4%) nucleotide differences between the two viruses. 15462 nucleotides comprised the JS genome in contrast to 15463 which constituted the genome of the prototype virus. This was accounted for by a single nucleotide deletion in the 5' non-coding region of the JS phosphoprotein gene. Four nucleotide substitutions were found in the leader region at the 3' end of the viral genome at positions 24, 28, 42 and 45, whereas no differences were found in the 44 base trailer region. All of the transcription start and stop signals and intergenic sequences were conserved between the two viruses with the exception of the transcription stop signal of the matrix (M) gene where there was a nucleotide transposition between bases 7 and 8. A comparison of all of the nucleotide differences in the 3' and 5' non-coding regions of each gene showed a variability of 9.8% and 10.5%, respectively. The 3' non-coding regions of the nucleocapsid (NP) and M genes were completely conserved in contrast to the polymerase (L) gene in which 25% of the nucleotides were different. Differences were observed in the 5' non-coding regions of each gene and ranged from 5.9% for the hemagglutinin neuraminidase (HN) gene to 14.6% for the M gene. An analysis of the amino acid differences in each open reading frame revealed that of all the genes, the coding region of the M gene was the most highly conserved (1.1% amino acid variability), while the phosphoprotein (P) gene was the most variable (5.8% amino acid variability). As these two viruses are wild type strains, these differences in nucleotide and amino acid sequence are compatible with efficient replication in vivo.

Base Sequence↗

PubMed1991

Cloning and sequencing of the fus-gene encoding elongation factor 2 in the archaebacterium Thermoplasma acidophilum.

We have cloned a 1.6-kb region of chromosomal DNA from Thermoplasma acidophilum into Escherichia coli using as a probe part of the Methanococcus vannielii fus-gene. The sequence of the clone was highly homologous to part of the corresponding Methanococcus vannielii gene. By chromosome walking, a 4.7-kb EcoRI fragment containing the complete gene was isolated. Nucleotide sequencing revealed an open reading frame of 2196 nucleotides. The deduced amino acid sequence contains the known peptide sequence around the ADP-ribosylation site of T. acidophilum elongation factor 2, which unequivocally confirms that the fus-gene has been cloned. The amino acid sequence was compared to that of hamster and E. coli, as well as to known archaebacterial EF-2 sequences.

Amino Acid Sequence↗

PubMed1996

Sequencing and expression of the human ALDH8 encoding a new member of the aldehyde dehydrogenase family.

The human aldehyde dehydrogenase gene (ALDH) family is characterized by two major conserved DNA sequences encoding residues which are possibly involved in the catalytic function and the maintenance of the functional conformation of the ALDH enzyme. This property is the basis for synthesizing the degenerate primers to clone several cDNAs of the ALDH isozymes. In this report, we describe the cDNA sequence and the expression of a new member of this family, ALDH8. The human ALDH8 gene was identified during the process of the screening for the human ALDH7 genomic clones. Overlapping ALDH8 cDNA clones were isolated by polymerase chain reaction (PCR) amplification of human salivary gland total RNA or lambda gt11 cDNA library. When the ALDH8 cDNA sequence was aligned with that of the ALDH7 which encodes a polypeptide chain of 468 amino acid (aa) residues, it was found that a termination codon (TGA) is placed in frame at the ALDH8 sequence corresponding to the codon GCG for the seventeenth aa position of the ALDH7. Therefore, the human ALDH8 gene is a potential nonprocessed pseudogene in the ALDH multigene family which has no other pseudogenes reported so far. Alternatively, the ALDH8 gene is a functional gene if the premature stop codon is suppressed, or if the first downstream in-frame ATG serves as the initiator codon. This longest putative open reading frame (ORF) encodes a polypeptide chain of 385 aa residues, includes the two ALDH conserved regions, and demonstrates 86% identity with the corresponding ORF region of the human ALDH7. The expression of the ALDH8 transcripts is restricted to the salivary gland among the human tissues examined.

Aldehyde Dehydrogenase↗

PubMed1992

Further characterization of the histidine gene cluster of Streptomyces coelicolor A3(2): nucleotide sequence and transcriptional analysis of hisD.

We have further characterized the genomic region of Streptomyces coelicolor A3(2) that contains genes involved in the biosynthesis of histidine. A 2,357-base pair fragment contained in plasmid pSCH3328 that complemented hisD mutations has been sequenced. Computer analysis revealed an open reading frame that encodes a protein with significant homology to the Escherichia coli, Salmonella typhimurium and Mycobacterium smegmatis hisD product, Saccharomyces cerevisiae HIS4C, and Neurospora crassa his3 gene products. Two other contiguous open reading frames oriented divergently with respect to hisD did not show significant similarity with any of the his genes or to other sequences included in the gene bank. S1 nuclease mapping and primer extension experiments indicate that the transcription initiation site of the his-specific mRNA coincides with the GUG translation initiation codon of the hisD cistron.

Base Sequence↗

PubMed1999

Gene structure and chromosomal localization of mouse S-adenosylmethionine decarboxylase.

The structure of the mouse S-adenosylmethionine decarboxylase (AdoMetDC) gene has been determined. The mouse gene (AMD1) consisted of eight exons and seven introns, similar to the rat AdoMetDC gene, and was mapped to chromosome 10. The characteristics of AMD1 gene were as follows: (1) The region of the promoter necessary for maximal transcriptional activity was located about 400 nucleotides upstream of the transcriptional initiation point, and contained a TATA box and two GC boxes. The transcriptional activity of the promoter was nearly equal to that of the SV40 promoter. (2) Two polyadenylation signals for transcription were observed, and the larger AdoMetDC mRNA, which is the dominant form of mRNA, corresponded to mRNA that is generated using the second polyadenylation signal. (3) Using stable transfectants, we confirmed that the upstream open reading frame (uORF) in the 5'-untranslated region (5'-UTR) of AdoMetDC mRNA functioned as a negative regulatory element. Lower concentrations of polyamines affect both stimulation and inhibition of AdoMetDC synthesis, through the uORF in the mRNA, than affect general protein synthesis.

5' Untranslated Regions↗

PubMed2006

Isolation and expression analysis of plastidic glucose-6-phosphate dehydrogenase gene from rice (Oryza sativa L.).

Glucose-6-phosphate dehydrogenase is a rate-limiting enzyme of pentose phosphate pathway, existing in cytosolic and plastidic compartments of higher plants. A novel gene encoding plastidic glucose-6-phosphate dehydrogenase was isolated from rice (Oryza sativa L.) and designated OsG6PDH2 in this article. Through semiquantitative RT-PCR approach it was found that OsG6PDH2 mRNA was weakly expressed in rice leaves, stems, immature spikes or flowered spikes, and a little higher in roots. However, the expression of OsG6PDH2 in rice seedlings was significantly induced by dark treatment. The complete opening reading frame (ORF) of OsG6PDH2 was inserted into pET30a (+), and expressed in Escherichia coli strain BL21 (DE3). The enzyme activity assay of transformed bacterial cells indicated that OsG6PDH2 encoding product had a typical function of glucose-6-phosphate dehydrogenase.

Amino Acid Sequence↗

PubMed1992

Nucleotide sequence analysis of a unique near-terminal region of the tumorigenic poxvirus, Shope fibroma virus.

Shope fibroma virus (SFV), a tumorigenic poxvirus, has a DNA genome of approximately 160 kb. Previous DNA sequence analysis of SFV has been mainly limited to the terminal inverted repetitions (about 12 kb at each end of the genome) and immediately adjacent regions. We have sequenced a 4 kb fragment located approximately 20 kb from the right-terminal hairpin. Within this region three complete and two partial open reading frames (ORFs) have been identified. Each of the putative polypeptides has sequence similarity to one or more previously identified poxvirus or cellular proteins, with homology to protein kinases, erythrocyte ankyrin and a vaccinia virus virulence-related protein (ORF N1L). The potential significance of these gene products with regard to the phenotype of SFV is discussed.

Amino Acid Sequence↗