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PubMed1996

Identification of a putative methylenetetrahydrofolate reductase by sequence analysis of a 6.8 kb DNA fragment of yeast chromosome VII.

We report the sequence analysis of a 6.8 kb DNA fragment from Saccharomyces cerevisiae chromosome VII. This sequence contains five open reading frames (ORFs) greater than 100 amino acids. There is also an incomplete ORF flanking one of the extremes, G2868, which is the 3' end of the SCS3 gene (Hosaka et al., 1994). The translated sequence of ORF G2882 shows similarity to the human methylenetetrahydrofolate reductase (Goyette et al., 1994). ORF G2889 shows no significant homologies with the sequences compiled in databases. ORF G2893 corresponds to the gene SUP44, coding for the yeast ribosomal protein S4 (All-Robin et al., 1990). G2873 and G2896 are internal ORFs.

Amino Acid Sequence↗

PubMed2004

Bioinformatics in reproductive biology--functional annotation based on comparative sequence analysis.

Recent studies of the genomes of a variety of model organisms have provided an unprecedented opportunity to identify and characterize all signaling molecules in the human genome. Regardless of the approaches used to decipher gene characteristics and their role in physiology, pairwise sequence comparison represents the fundamental bioinformatic tool for initial functional annotation of newly identified genes. Because genes evolved from duplication and adapted to different evolutionary niches for each organism during speciation, detailed sequence analysis could provide additional information on the biochemical and biological characteristics of novel genes. In addition, the integration of sequence-based gene discovery with phylogeny-based function prediction leads to a more complete understanding of the signaling pathways. For example, detailed pairwise sequence analysis has led to the identification of (1) stresscopin (SCP) and stresscopin-related peptides (SRP) as the CRH-related genes, (2) multiple relaxin-like factor genes, and (3) the novel glycoprotein hormone subunit family genes, alpha2 and beta5. Furthermore, based on the understanding that ligands and receptors coevolved during evolution, we have identified a variety of novel extracellular signaling polypeptides including (1) stresscopin and stresscopin-related peptides as selective ligands for the type 2 CRH receptor, (2) the pregnancy hormone, relaxin, and related peptides that activate two orphan G protein-coupled receptors (GPCRs), LGR7 and LGR8, and (3) alpha2 and beta5 that form a heterodimer capable of activating the TSH receptor. Thus, detailed studies on the characteristics and evolution of gene sequences have provided an inroad to the elucidation of novel signaling polypeptides and the associated signal transduction pathways.

Animals↗

PubMed2005

Prevalence of four virulence genes in Campylobacter jejuni determined by PCR and sequence analysis.

INTRODUCTION: The presence of four virulence genes (racR, wlaN, cgtB, virB11) in 356 Campylobacter jejuni strains isolated from confirmed clinical cases was examined by PCR and sequence analysis. The investigated genes were chosen on the basis of their variation in prevalence. METHODS: The virulence genes were detected by PCR and the amplified products were submitted for sequence analysis. RESULTS: The gene with the highest prevalence was racR (87.08%). virB was present in only 1.69% of the C. jejuni strains, and wlaN and cgtB were detected in 16.01% and 24.44%, respectively. Five strains associated with Guillain-Barré syndrome and Miller-Fischer syndrome out of the total of 356 (1.40%) were positive for cgtB. CONCLUSION: Our findings suggest that racR may encode factors necessary for bacterial pathogenicity in humans, while the roles of the other three genes remain ambiguous.

Campylobacter jejuni↗

PubMed1996

Taxonomic characterization of closely related Streptomyces spp. based on the amino acid sequence analysis of protease inhibitor proteins.

Amino acid sequences of protease inhibitors (Streptomyces subtilisin inhibitor-like proteins) widely distributed in Streptomyces were compared to clarify the taxonomic status of three strains of Streptomyces spp., S. coelicolor A3(2), S. lividans 66 and S. coelicolor Müller, which are closely related by conventional taxonomical procedures. The sequence comparison indicated that S. coelicolor A3(2) is distinct from the type strain S. coelicolor Müller, but belongs to the same taxon as S. lividans 66.

Amino Acid Sequence↗

PubMed1999

Phylogenetic characterization of Centipeda periodontii, Selenomonas sputigena and Selenomonas species by 16S rRNA gene sequence analysis.

The nearly complete 16S rRNA gene sequences for oral Gram-negative anaerobic motile bacteria, Centipeda periodontii, Selenomonas sputigena and Selenomonas species (formerly S. sputigena type strain), were determined in order to unveil their relationship to other oral motile bacteria. To determine the phylogenetic characterization of these bacteria, their 16S rRNA gene sequences were obtained and compared with those from the ribosomal sequence databases previously reported. The 16S rRNA gene sequences of these bacteria were similar to those of Selenomonas ruminantium and Schwartzia succinivorans isolated from rumens, and to Pectinatus cerevisiiphilus isolated from spoiled beer. Among oral bacteria, the nucleotide sequence analysis of these bacteria revealed high nucleotide similarity to Veillonella species, whereas low similarity to oral motile bacteria such as Campylobacter species. Phylogenetic analysis clearly confirmed that C. periodontii and two Selenomonas species were classified as relatives of a group besides Selenomonas, Schwartzia, and Pectinatus species, and not as close relatives to oral motile bacteria, such as Campylobacter species. These results suggest that such oral Gram-negative anaerobic motile bacteria are close relatives of oral bacteria.

Phylogeny↗

PubMed1984

A DNA sequence analysis package for the IBM personal computer.

We present here a collection of DNA sequence analysis programs, called "PC Sequence" (PCS), which are designed to run on the IBM Personal Computer (PC). These programs are written in IBM PC compiled BASIC and take full advantage of the IBM PC's speed, error handling, and graphics capabilities. For a modest initial expense in hardware any laboratory can use these programs to quickly perform computer analysis on DNA sequences. They are written with the novice user in mind and require very little training or previous experience with computers. Also provided are a text editing program for creating and modifying DNA sequence files and a communications program which enables the PC to communicate with and collect information from mainframe computers and DNA sequence databases.

Amino Acid Sequence↗

PubMed1999

Genetic polymorphism near HIV-1 reverse transcriptase resistance-associated codons is a major obstacle for the line probe assay as an alternative method to sequence analysis.

The performance of the line probe assay (LIPA) for the detection of mutations conferring resistance to nucleoside inhibitors of HIV-1 reverse transcriptase was evaluated in comparison with sequence analysis. The tests were undertaken on plasma samples from 63 patients (61 receiving combination therapy and 2 without treatment at the time of inclusion). In 27 cases (43%) which included codons 41, 69, 70, 74, 184 and 215, the sequence of the RT gene was distinct from the hybridization probes used in LIPA. Correspondingly, LIPA gave uninterpretable results in 15, 30 and 41% of cases for codons 184, 215 and 41, respectively. Overall, the concordance between LIPA and sequence analysis varied from 52% (codons 41 and 215) to 85% (codon 70). These data show that the polymorphism of the nucleotide sequence near resistance-associated codons is a major shortcoming of LIPA.

Codon↗

PubMed2001

Comparison of sequence analysis of 16S-23S rDNA spacer regions, AFLP analysis and DNA-DNA hybridizations in Bradyrhizobium.

The sequences of the 16S-23S rDNA intergenic spacer region of 62 strains of Bradyrhizobium, including representatives of the three valid species, were determined. The majority of strains had a single rRNA operon type and all contained a tRNA(Ala) and a tRNA(Ile) gene. Analysis of the sequence data produced groupings in line with previously obtained AFLP data. DNA-DNA hybridizations were performed to determine to what extent spacer sequences and AFLP profiles reflected the overall genomic similarities. Strains belonging to the same AFLP group, and strains with spacer sequences diverging less than 4%, were found to belong to the same genospecies. More remote relationships (DNA homology levels of 40-60%) between species were reflected in the spacer sequence analysis, but not in the AFLP analysis. For the genus Bradyrhizobium, 16S-23S rDNA spacer sequence analysis provides taxonomic information similar, but not always identical to that obtained by DNA-DNA hybridizations. Our results indicate that this genus consists of a group of four highly related genospecies (Bradyrhizobium japonicum, Bradyrhizobium liaoningense and two other genospecies) and at least three other genospecies, one of which is Bradyrhizobium elkanii.

Bradyrhizobium↗

PubMed1995

Cloning and sequence analysis of the aminopeptidase My gene from Mycoplasma salivarium.

The complete nucleotide sequence of a major component of aminopeptidase My purified from Mycoplasma salivarium was determined. The protein gene encoded a protein consisting of 520 amino acids with a molecular mass of 58079 Da. The protein contained two tryptophan residues, one of which was encoded by UGA. A computer-aided homology search suggested that aminopeptidase My had properties similar to those of leucine aminopeptidase (EC 3.4.11.1).

Amino Acid Sequence↗

PubMed1994

Sequence analysis and mapping of a novel human mitochondrial ATP synthase subunit 9 cDNA (ATP5G3).

We describe the cloning, sequence analysis, and chromosomal mapping of a novel mitochondrial ATP synthase subunit 9cDNA, P3. Subunit 9 transports protons across the inner mitochondrial membrane to the F1-ATPase protruding on the matrix side, resulting in the generation of ATP. Sequence analysis of the P3 cDNA reveals only 80% identity with the human subunit 9 genes P1 and P2 in the DNA sequence encoding the mature peptide. However, this sequence predicts a mature protein identical to P1 and P2. The predicted sequence of the P3 leader peptide differs from the P1 and P2 leaders, but retains the "RFS" motif critical for mitochondrial import and maturation. The P3 gene (ATP5G3) maps to chromosome 2.

Amino Acid Sequence↗

PubMed2004

Fluorescent modification of N-terminal amino group in peptides for complete sequence analysis using PSD method in MALDI-TOF-MS.

In the sequence analyses of peptides from nucleoprotein in influenza virus, it was very difficult to obtain the sufficient numbers of fragment ions using the post-source decay (PSD) method in MALDI-TOF-MS. Fluorescent modification of the N-terminal amino group in the target peptides was introduced for the PSD measurement. The fluorescently-labelled peptides gave sufficient fragment ions in the PSD spectrum, which leads to the complete sequence analysis of peptide.

Amines↗

PubMed1997

HLA class II haplotype and sequence analysis support a role for DQ in narcolepsy.

A systematic haplotype and sequencing analysis of the HLA-DR and -DQ region in patients with narcolepsy was performed. Five new (CA)n microsatellite markers were generated and positioned on the physical map across the HLA-DQB1-DQA1-DRB1 interval. Haplotypes for these new markers and the three HLA loci were established using somatic cell hybrids generated from patients. A four-marker haplotype surrounding the DQB1(*)0602 gene was found in all narcolepsy patients, and was identical to haplotypes observed on random chromosomes harboring the DQB1(*)0602 allele. Eighty-six kilobases of contiguous genomic sequence across the region did not reveal new genes, and analysis of this sequence for single nucleotide polymorphisms did not reveal sequence variation among DQB1(*)0602 chromosomes. These results are consistent with other studies, suggesting that the HLA-DQ genes themselves are among the predisposing factors in narcolepsy.

Causality↗

PubMed2002

Isolation and sequence analysis of the rat dihydrolipoamide succinyltransferase gene.

The dihydrolipoamide succinyltransferase (DLST) gene of the alpha-ketoglutarate dehydrogenase complex (alpha-KGDC) was isolated from a rat genomic DNA library and sequenced. This gene was composed of 15 exons and 14 introns like the human DLST gene. Sequence analysis of the promoter-regulatory region of the rat DLST gene-(Dlst) showed the possible presence of a CAAT box-sequence and of the sequences for an AP-2 site and three Sp1 sites, but no TATA box-sequence was evidenced. The nucleotide sequences of introns 1 and 4 of the rat Dlst were significantly homologous to those of introns 1 and 4 of the human DLST gene. The sequence analysis of the rat Dlst suggested that the exon coding for the E3- and/or E1-binding domain may have been lost from the gene during evolution in eukaryotic DLST, possibly after mitochondrial symbiosis because prokaryotic DLST possesses the E3- and/or E1-binding domain.

Acyltransferases↗

PubMed1977

Sequence analysis of oligodeoxyribonucleotides by mass spectrometry. 2. Application of computerized pattern recognition to sequence determination of di-, tri-, and tetranucleotides.

A novel strategy for the sequence analysis of oligodeoxyribonucleotides has been devised which is based upon the analysis of intact underivatized oligonucleotides by mass spectrometry followed by interpretation of the mass-spectral data by computerized pattern-recognition techniques. The pyrolytic and electron-impact conditions of the mass spectrometer permit the cleavage of oligonucleotides of varying chain length and composition, yielding reproducible fragmentations and characteristic m/e values which can be used to reveal purine and/or pyrimidine base sequence information. The selection of optimum features (which are the ratios of peak heights of specific ions, or the linear combination of such ratios) has been done by an interactive feature selection method employing multidimensional k nearest-neighbor analysis and two-dimensional feature-space plots (nonlinear mappings) of the mass-spectral data. Features have been found which allow 100% classification accuracy in predicting the 5' and 3' terminus of all of the dinucleotides commonly found in DNA. Other specific features have been found which indicate adjacent nucleotides within a tetranucleotide. Knowledge of the adjacent nucleotide pairs present, in conjunction with the information as to the 3' or 5' position of the residues in each pair, permits the reconstruction of the sequence of the tetranucleotide.

Base Sequence↗

PubMed1990

Nucleic acid sequence analysis software for microcomputers.

It is clear that a computer-aided data control system is required for even small laboratories generating nucleic acid data. While the molecular biologist at many universities and large research institutions has access to mainframe computers and nucleic acid sequence analysis software, many find it more convenient to perform sequence analysis on microcomputers that are typically located within the investigator's laboratory and totally dedicated to sequence storage and analysis, in essence giving the investigator more personal control of analysis activities than is sometimes possible with shared mini- or mainframe computers. New programs are being written and released at an increasing rate to perform increasingly more complex and specialized analyses using small computer-based systems. This trend will undoubtedly continue, fueled by the need to manage the ever increasing quantity of sequence data.

Base Sequence↗

PubMed2002

Cloning and sequence analysis of the complementary DNA for feline preproparathyroid hormone.

OBJECTIVES: To clone and sequence the cDNA for feline preproparathyroid hormone (preproPTH) and to compare that sequence with other known parathyroid hormone (PTH) sequences. SAMPLE POPULATION: Parathyroid glands from 1 healthy cat. PROCEDURES: A cDNA library was constructed in lambda phage from feline parathyroid gland mRNA and screened with a radiolabeled canine PTH probe. Positive clones were sequenced, and nucleic acid and deduced amino acid sequences were analyzed and compared with known preproPTH and PTH sequences. RESULTS: Screening of approximately 2 X 10(5) recombinant plaques revealed 3 that hybridized with the canine PTH probe; 2 clones comprised the complete sequence for feline preproPTH. Feline preproPTH cDNA consisted of a 63-base pair (bp) 5'-untranslated region (UTR), a 348-bp coding region, and a 326-bp 3'-UTR. The coding region encoded a 115-amino acid peptide. Mature feline PTH consisted of 84 amino acids. Amino acid sequence analysis revealed that feline PTH was > 83% identical to canine, bovine, swine, equine, human, and macaque PTH and 69, 71, and 44% identical to mouse, rat, and chicken PTH, respectively. Within the region responsible for hormonal activity (amino acids 1 to 34), feline PTH was > 79% identical to other mammalian PTH sequences and 64% identical to the chicken sequence. CONCLUSIONS AND CLINICAL RELEVANCE: The amino acid sequence of PTH is conserved among mammalian species. Knowledge of the cDNA sequence for feline PTH may be useful to investigate disturbances of calcium metabolism and alterations in PTH expression in cats.

3' Untranslated Regions↗

PubMed1985

Rat liver glutathione S-transferases. Nucleotide sequence analysis of a Yb1 cDNA clone and prediction of the complete amino acid sequence of the Yb1 subunit.

We have constructed a nearly full length cDNA clone, pGTA/C44, complementary to the rat liver glutathione S-transferase Yb1 mRNA. The nucleotide sequence of pGTA/C44 has been determined, and the complete amino acid sequence of the Yb1 subunit has been deduced. The cDNA clone contains an open reading frame of 654 nucleotides encoding a polypeptide comprising 218 amino acids with Mr = 25,919. The NH2-terminal sequence deduced from DNA sequence analysis of pGTA/C44 is in agreement with the first 19 amino acids determined for purified glutathione S-transferase A, a Yb1 homodimer, by Frey et al. (Frey, A. B., Friedberg, T., Oesch, F., and Kreibich, G. (1983) J. Biol. Chem. 258, 11321-11325). The DNA sequence of pGTA/C44 shares significant sequence homology with a cDNA clone, pGT55, which is complementary to a mouse liver glutathione S-transferase (Pearson, W. R., Windle, J. J., Morrow, J. F., Benson, A. M., and Talalay, P. (1983) J. Biol. Chem. 258, 2052-2062). We have also determined 37 nucleotides of the 5'-untranslated region and 348 nucleotides of the 3'-untranslated region of the Yb1 mRNA. The Yb1 mRNA and subunit do not share any sequence homology with the rat liver glutathione S-transferase Ya or Yc mRNAs or their corresponding subunits. These data provide the first direct evidence that the Yb1 subunit is derived from a gene or gene family which is distinct from the Ya-Yc gene family.

Amino Acid Sequence↗

PubMed2006

Performance of sequence analysis, INNO-LiPA line probe assays and AFFIGENE assays in the detection of hepatitis B virus polymerase and precore/core promoter mutations.

In this study, we compare results obtained by sequences analysis and commercial kits in the detection of hepatitis B virus (HBV) polymerase and precore (PC) and core promoter mutations. A total of 23 serum samples from lamivudine treated patients were tested for polymerase mutations by direct sequencing, INNO-LiPA HBV DR and AFFIGENE HBV DE/3TC. Full concordance among the three assays was observed in 63% of the total analysed codons. Concordant results were obtained between sequencing and LiPA in 80%, between sequencing and AFFIGENE in 73% and between LiPA and AFFIGENE in 74% of all tested codons. All discrepancies were observed in mixed population samples in which AFFIGENE and LiPA detected additional viral variants not revealed by sequence. In two patients, with serial samples, LiPA detected earlier than sequence and AFFIGENE an emerging mutate strain. PC and core promoter viral variants were detected in 28 serum samples collected from 14 HBV inactive carriers and from 14 hepatitis B patients with chronic liver disease. Direct sequencing, INNO-LiPA HBV PreCore and AFFIGENE HBV MUTANT VL 19 showed fully coincident results in 88% of tested positions. These findings showed that all assays evaluated were sensitive and accurate tools to analyse HBV genomic variability. Sequence analysis is essential to study new emerging mutations as LiPA and AFFIGENE assays are more easily useful in clinical laboratories to detect the appearance of well-characterized HBV variants.

DNA Probes↗