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PubMed1984

A fusion gene in man: DNA sequence analysis of the abnormal globin gene of hemoglobin Miyada.

An abnormal globin gene from a patient heterozygous for Hemoglobin Miyada was cloned and sequenced. The results indicated that the 5' flanking region and the 5' side of the gene were identical to those of a beta-globin gene and that the 3' side was identical to that of a delta-globin gene. The part of the gene identical to a beta-globin gene shifted to the part identical to the delta-globin gene somewhere in a homologous sequence region between the third nucleotide of the 17th codon and the second nucleotide of the 22nd codon of these two genes. Thus, results of analysis of the nucleotide sequence support the idea that the abnormal globin gene of Hemoglobin Miyada was generated as a fusion gene by unequal crossing over between a beta- and a delta-globin gene.

Amino Acid Sequence↗
PubMed1992

Identification by DNA sequence analysis of a new plasmid-encoded trimethoprim resistance gene in fecal Escherichia coli isolates from children in day-care centers.

In our ongoing studies of trimethoprim resistance (Tmpr) in day-care centers (DCC), we have shown a high rate of fecal colonization with Tmpr Escherichia coli and, using total plasmid content analysis, have shown that this is due to a diversity of strains. In the present study, we analyzed 367 highly Tmpr (MIC, greater than or equal to 2,000 micrograms/ml) isolates of E. coli from 72 children over a 5-month period and found at least 83 distinct plasmid patterns, indicating that at least 83 strains were involved. Several strains were particularly common in a given DCC, including one found in 61% of children with Tmpr E. coli; these common strains usually persisted within a DCC for several months. Colony lysates were hybridized with gene probes for dihydrofolate reductases (DHFR) types I, II, III, V, and VII; 21% hybridized under stringent conditions, and all of these were with type I (17%) or type V (4%) probes. Tmpr was cloned from a probe-negative Tmpr transconjugant, and an intragenic probe was prepared from this clone. Approximately 21% of the Tmpr E. coli strains (76 isolates) in the DCC were found to have this new gene, 74 of which were in one DCC. The DNA sequence of this gene was determined, and the predicted amino acid sequence was shown to have between 32% and 39% identity with the amino acid sequences for types I, III, V, VI, and VII and the partial sequence of type IV and approximately 26% identity with types IX and X DHFR. This confirms the uniqueness of this gene, which has tentatively been named dhfrxii, and its translation product, DHFR type XII.

Amino Acid Sequence↗
PubMed1991

DNA sequence analysis of NKG2, a family of related cDNA clones encoding type II integral membrane proteins on human natural killer cells.

We have previously described the isolation of a cDNA clone, designated NKG2, that was expressed in all natural killer (NK) cells tested but not in T or B cells. In the present communication, the original isolate, when used to probe a cDNA library prepared from a CD3- NK cell clone, was found to crosshybridize with a family of transcripts that fell into four distinct groups designated NKG2-A, -B, -C, and -D. Full-length cDNA sequences were determined for each group, and the DNA and inferred peptide sequences were analyzed. All four transcripts encode type II membrane proteins of 215-233 amino acids. NKG2-A and -B peptides appear to be alternative splicing products of a single gene. NKG2-C is highly homologous with group A, having 94% homology in the external (COOH-terminal) domain and 56% homology throughout the internal and transmembrane regions. NKG2-D is distantly but significantly related (21% amino acid homology) to the first three groups. Therefore, NKG2-A, -C, and -D appear to be encoded by distinct genes within a family of NK cell-specific genes. Peptide sequence homology searches demonstrate that the NKG2 peptides are members of a supergene family that includes several other type II membrane proteins. This family is characterized by the presence of a C-type animal lectin domain, and several of its members have demonstrated transmembrane signaling capability.

Amino Acid Sequence↗
PubMed1986

A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11.

A computer package written in Fortran-IV for the PDP-11 minicomputer is described. The package's novel features are: software for voice-entry of sequence data; a less memory intensive algorithm for optimal sequence alignment; and programs that fit statistical models to nucleic acid and protein sequences.

Base Sequence↗
PubMed1987

DNA sequence analysis of the Dutch beta zero-thalassemia deletion.

The Dutch beta zero-thalassemia has relatively few clinical symptoms in the homozygote. Heterozygotes have levels of fetal hemoglobin (4-11%) comparable to delta beta-thalassemia, and much higher than in typical beta zero-thalassemia. To analyze this deletion, we have cloned the abnormal 10 kb Bgl II fragment that contains the delta-globin gene into phage lambda vector EMBL4. A Hind III-Xba I fragment that includes the endpoints of the deletion was subcloned into plasmid pUC 19 and partially sequenced by the dideoxy method. The sequence of the Dutch beta zero-thalassemia DNA is like that of normal 5' DNA to 8920 (the numbering system is from reference 2). The sequence from 8915-8920 is AAATTT, which is also the normal 3' sequence from 21537-21542. From this point on, the Dutch beta zero-thalassemia sequence is like that of the normal 3' DNA. The deletion is therefore 12.6 kilobases, rather than 10 as originally estimated. It is similar to several other beta-globin gene deletions in terminating in a region of Kpn I repeated sequences, and having several base pairs of homology between 5' and 3' sequences at the break points.

Base Sequence↗
PubMed1986

DNA sequence analysis: a procedure to find homologies among many sequences.

SEQCMP, a program that analyzes and searches for homology among multiple nucleic acid sequences, is described. The sequences are compared by the dot matrix method and the consensus sequence is derived by superimposing all the dot matrices on one another. The program is written in MBASIC and runs on IBM-PC microcomputer. It is interactive and can be used by investigators with no computer background or experience.

Base Sequence↗
PubMed1996

DNA sequence analysis and restriction fragment length polymorphisms of the P1 gene of Haemophilus influenzae biogroup aegyptius associated with Brazilian purpuric fever.

Brazilian purpuric fever (BPF) is a fulminant pediatric disease caused by specific strains of Haemophilus influenzae biogroup aegyptius. A conserved epitope on the P1 protein of strains of H. influenzae biogroup aegyptius is seen on most virulent isolates. The P1 protein from a Brazilian case-clone strain of H. influenzae biogroup aegyptius was analyzed by cloning and sequencing the gene. Three major variable regions are present within the P1 gene of the BPF clone in an architecture similar to that of the previously sequenced P1 genes from H. influenzae. The DNA sequence data of the P1 gene provided information for restriction fragment length polymorphism analyses among strains of H. influenzae biogroup aegyptius. Using PCR for amplification of the P1 gene, we found that AlwI restriction of this gene allowed for a highly accurate segregation of virulent strains of H. influenzae biogroup aegyptius associated with BPF. The strong association of virulent phenotypes with specific AlwI restriction patterns of the P1 gene provides a basis for the convenient and accurate identification of strains of H. influenzae biogroup aegyptius which cause BPF.

Bacterial Outer Membrane Proteins↗
PubMed1984

BIOLOG - a DNA sequence analysis system in PROLOG.

BIOLOG contains facilities for the analysis of nucleic acid sequences. These facilities are available through queries and commands of the underlying implementation language PROLOG. Familiarity with PROLOG is gained by using the built-in BIOLOG functions. This experience should enable the user to extend the current system and define new facilities.

Amino Acid Sequence↗
PubMed1987

Linkage, physical mapping, and DNA sequence analysis of pseudoautosomal loci on the human X and Y chromosomes.

The pseudoautosomal region of the human X and Y chromosomes is subject to frequent X-Y recombination during male meiosis. We report the finding of two pseudoautosomal loci, DXYS20 and DXYS28, characterized by highly informative restriction fragment length polymorphisms (RFLPs). The pseudoautosomal character of DXYS20 and DXYS28 was formally demonstrated by comparing their transmission to 45,X and to normal individuals. Studies of the inheritance of these loci reveal that the pseudoautosomal region, though highly recombinogenic, is subject to marked recombinational interference in male meiosis; no double recombinants were observed in 143 triply informative meioses, and the coefficient of coincidence is likely less than 0.45. In female meiosis, linkage of these pseudoautosomal RFLPs to strictly sex-linked RFLPs on the short arm of the X is readily detected; the genetic length of the pseudoautosomal region in female meiosis is at least 4 cM but not more than 18 cM. The genetic map of the human X chromosome is now defined from near the short-arm telomere to band q28 on the long arm. Locus DXYS20, which maps near the X and Y short-arm telomeres, is composed of long tandem arrays of 61-bp repeats. Occasional, seemingly random base-pair substitutions within these arrays of 61-bp repeats, in combination with marked variation in the size of the array, generate the high degree of DNA polymorphism at DXYS20.

Base Sequence↗
PubMed1992

Mitochondrial DNA sequence analysis of the cytochrome oxidase subunit I and II genes, the ATPase9 gene, the NADH dehydrogenase ND4L and ND5 gene complex, and the glutaminyl, methionyl and arginyl tRNA genes from Trichophyton rubrum.

In this paper, we present the nucleotide sequence of a 5248 bp-long region of the mitochondrial (mt) genome of the dermatophyte Trichophyton rubrum. This region which represents about 1/4 of the total mt genome of this species reveals a compact organization of genes including: the glutaminyl tRNA, the methionyl tRNA, the cytochrome oxidase subunit I gene, the arginyl tRNA, the mitochondrial version of the ATPase subunit 9 gene, the cytochrome oxidase subunit II gene and a part of the NADH dehydrogenase ND4L and ND5 gene "complex". The main features of the part of mt DNA sequenced is the non-interrupted COXI gene and the presence in the mitochondrial version of the ATPase 9 gene of a small group IA intron. The extensive amino-acid sequence similarity with the equivalent gene in Aspergillus nidulans and Neuropora crassa indicates that this gene codes for a dicyclohexylcarbodiimide binding protein. The conserved arrangement of this portion of the mt genome and the presence of tRNAs between the protein-coding genes are compatible with a large polycistronic transcript processed by the excision of tRNAs, or similar secondary structures, as proposed for other fungal or mammalian mt DNAS.

Adenosine Triphosphatases↗
PubMed1987

DNA sequence analysis of spontaneous mutation in a PolA1 strain of Escherichia coli indicates sequence-specific effects.

The sequences of a collection of 261 spontaneous lacI- mutants recovered in a PolA- strain of Escherichia coli have indicated an increase in the frequency of most classes of mutation in this strain. Among base substitutions in lacI, a preference for transversions over transitions was observed. In addition, a single transition in the lac operator was enhanced 8-fold. More significantly, of 18 frameshifts, 12 occurred adjacent to a 5'-GTGG-3' sequence. Likewise, 15 of 24 deletions and 2 of 10 duplications had 5'-GTGG-3' sequences at one or both endpoints. We speculate that the prevalence of mutations at these specific sequences reflects the persistence of strand discontinuities that enhance the opportunity for mutagenic mishaps. Further, 5'-GTGG-3' sequences apparently represent sites where DNA polymerase I is involved in some aspect of DNA metabolism. These results strengthen the view that DNA context contributes an important component to spontaneous mutagenesis and indicate an anti-mutagenic role for DNA polymerase I.

Base Sequence↗
PubMed1993

The DNA sequence analysis of the HAP4-LAP4 region on chromosome XI of Saccharomyces cerevisiae suggests the presence of a second aspartate aminotransferase gene in yeast.

The nucleotide sequence of a 19,000 base pair region from the left arm of chromosome XI of Saccharomyces cerevisiae has been determined and analysed. It covers the HAP4-GFA1-LAP4 loci already described. As expected HAP4, GFA1 and LAP4 genes have been found and six new open reading frames (ORFs) with a coding capacity of more than 100 amino acid residues have been identified. One of them (YKL461) shows a high degree of identity with an aspartate aminotransferase gene. This raises the question of a second aspartate aminotransferase gene in yeast. A second ORF (YKL462) shows features compatible with a membranous localization. The other ORFs do not show a similarity with any known gene. A member of the highly repetitive 'CAT' DNA sequence is present.

Aspartate Aminotransferases↗
PubMed2005

DNA sequence analysis of the genetic environment of various blaCTX-M genes.

OBJECTIVES: Over a 3 year period (2000-2003) 21 Escherichia coli, 5 Klebsiella pneumoniae, 1 Serratia marcescens and 1 Proteus mirabilis producing CTX-M-type beta-lactamase were collected from five different hospitals in Paris, France. This study was conducted to analyse the genetic environment of these 28 bla(CTX-M) genes. METHODS: Antimicrobial susceptibility testing was performed by the disc diffusion method and MICs of various beta-lactams were determined by an agar dilution method. PCR was used to detect and sequence alleles encoding CTX-M, TEM, SHV and CMY enzymes. The genetic environment was analysed by amplification and direct sequencing using various set of PCR primers or cloning in pBK-CMV. RESULTS: Sequence analysis revealed that these isolates contained seven different bla(CTX-M) genes: bla(CTX-M-1) (4 strains), bla(CTX-M-2) (2 strains), bla(CTX-M-3) (4 strains), bla(CTX-M-9) (1 strain), bla(CTX-M-14) (5 strains), bla(CTX-M-15) (11 strains), bla(CTX-M-24) (1 strain). TEM-1 was associated with CTX-M-type enzymes in 15 isolates. Two strains produced both CTX-M-15 and SHV-2 or CTX-M-14 and CMY-2. In 25 strains the insertion sequence ISEcp1 was located upstream of the 5' end of the bla(CTX-M) gene. Among these strains, in five isolates, ISEcp1 was disrupted by insertion sequences such as IS26 (in three of them) or IS1 or IS10. Insertion sequence IS903 was found downstream of bla(CTX-M-14) or bla(CTX-M-24). Examination of the other three bla(CTX-M) genes (two bla(CTX-M-2) and one bla(CTX-M-9)) by cloning, sequencing and PCR analysis revealed the presence of complex Class 1 integrons, In35, an integron similar to In60 and a novel integron. CONCLUSIONS: This work further confirmed the predominant role of ISEcp1 in the mobilization of bla(CTX-M) genes of the CTX-M-1 cluster and the presence of In35, of an integron similar to In60 and a novel complex Class 1 integron.

Base Sequence↗
PubMed1997

Identification and DNA sequence analysis of the Marek's disease virus serotype 2 gene homologous to the herpes simplex virus type 1 glycoprotein H.

Marek's disease virus (MDV) serotype 2 (MDV2) gene homologous to the glycoprotein H (gH) gene of herpes simplex virus type 1 was identified and sequenced. The predicted region encoding for the MDV2 gH gene was 2436 nucleotide and the primary translation product was 812 amino acids with a molecular weight of 89.4 kDa. The protein encoded by MDV2 gH gene has a number of features characteristic of a membrane-associated glycoprotein. First, there are 9 potential N-linked glycosylation sites and 11 cysteine residues, and 6 of the sites and 8 of the residues were conserved among all of the three MDV serotypes. Second, this protein had N-terminal and C-terminal hydrophobic regions, which were a signal sequence and a transmembrane-anchor domain, respectively. From the northern blot analysis, it was suggested that a transcript encoding MDV2 gH and a poly-cistronic transcript encoding MDV2 thymidine kinase, gH, and possibly other genes of downstream on this strand existed. Alignment of the amino acid sequences of the gH homologues among the three MDV serotypes showed 57.5% (MDV1 and MDV2), 56.2% (MDV1 and HVT), and 50.1% (MDV2 and HVT) identities.

Amino Acid Sequence↗
PubMed1990

Cloning and DNA sequence analysis of a polygalacturonase cDNA from Aspergillus niger RH5344.

A 1319 bp long cDNA encoding for a polygalacturonase (EC 3.2.1.15) from Aspergillus niger RH5344 comprises a single open reading frame of 1089 bp which includes the mature protein of 362 amino acids and an NH2-terminal signal peptide of 27 amino acids. The directly determined peptides of the mature polygalacturonase confirmed the sequence information deduced from the cDNA.

Amino Acid Sequence↗
PubMed1985

Primary structure of the telopeptide and a portion of the helical domain of chicken type II procollagen as determined by DNA sequence analysis.

A comparison of the nucleotide sequences of three new cDNA clones for chicken type II procollagen with the sequences of the other three types of chicken fibrillar procollagens reveals that the most conserved regions correlate with the positions of hydroxyproline, hydroxylysine, cysteine and lysine residues. On the basis of replacement-site-divergence calculations it is concluded that alpha 1(II) and alpha 1(I) procollagens diverged later than alpha 1(I) and alpha 2(I) procollagens.

Amino Acid Sequence↗
PubMed1990

Application of a new method of pattern recognition in DNA sequence analysis: a study of E. coli promoters.

An algorithm from the pattern recognition theory 'generalized portrait' was used to find a distinguishing vector (scoring matrix) for E. coli promoters. We have attempted to solve three closely linked problems: (i) the selection of significant features of the signal; (ii) subsequent multiple alignment and (iii) calculation of the vector coordinates. Promoters with known strength have been successfully ranked in the correct order using this vector. We demonstrate the use of this method in predicting the location of promoters. A revised consensus promoter sequence is also presented.

Algorithms↗