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PubMed2002

Molecular cloning and sequencing of cDNA encoding for human FA-1 antigen.

The cDNA encoding for the human FA-1 sperm antigen was cloned and sequenced from the in-house constructed subtractive human testis cDNA expression library in lambda Ziplox using the FA-1 monoclonal antibody (mAb). The full--length sequence was obtained by using the 5' rapid amplification of 5'-cDNA end (5'-RACE) procedure. It is 1,576-bp long, and has an open reading frame (ORF) of 283 amino acids (aa) with the first ATG Met start codon at nucleotide (nt) 57 and the stop codon TAG at nt 906. It has two termination codons at the 5' end before the ATG start codon. The translated protein has a calculated molecular weight of 32.1 kDa and estimated isoelectric point (pI) of 11.59. It has one potential N-linked glycosylation site and one tyrosine phosphorylation site, besides several O-linked glycosylation and serine and threonine phosphorylation sites. Hydrophilicity analysis of the deduced aa sequence showed it to be a membrane-anchored protein. Extensive computer search in the database did not identify any known nt/aa sequence having homology with FA-1 cDNA or deduced aa, indicating it to be a novel gene. The Northern blot and reverse transcription-polymerase chain reaction (RT-PCR)-Southern blot analyses indicated the testis-specific expression of FA-1 antigen at the mRNA level. The ORF of the FA-1 was subcloned into pGEX- 1lambda T for expression. The expressed FA-1 recombinant protein had a molecular size of approximately 40 kDa, and was recognized by the FA-1 mAb, and not by the myeloma control Ig. The rabbit antibodies (Ab) raised against the recombinant (r) FA-1 antigen recognized the rFA-1 antigen as well as the native (n) FA-1 antigen. The rFA-1 Ab specifically recognized a protein band of approximately 50 kDa in human testis extract in the Western blot involving 11 types of human tissue extracts, indicating the testis-specific expression of FA-1 at the protein level. The Ab showed binding with live and methanol-fixed human sperm at the post-acrosomal, mid-piece, and tail regions. The Ab caused a significant (P < 0.001) and concentration-dependent inhibition of human sperm capacitation/acrosome reaction by blocking tyrosine phosphorylation of the FA-1 antigen. The sperm-specific human FA-1 recombinant antigen may find applications in immunocontraception, and diagnosis and treatment of immunoinfertility in humans.

Acrosome Reaction↗
PubMed2001

Molecular cloning and sequencing of a novel cDNA encoding for a protein involved in human sperm function.

A cDNA encoding for an antigen, designated as NZ-3, was cloned and sequenced from human testis. The 1481-bp NZ-3 cDNA yielded an open reading frame (ORF) of 231 amino acids (aa) with the first ATG, Met start codon at nucleotide (nt) 104 and the stop codon TGA at nt 797. Extensive computer search indicated it to be a novel cDNA/protein. The ORF of NZ-3 cDNA was subcloned into pGEX-1lambdaT vector and expressed in glutathione S-transferase gene fusion system. The expressed recombinant protein had a molecular size of approximately 25 kDa, and the rabbit antibodies (Ab) against the recombinant antigen recognized a specific protein band of 63 +/- 3 kDa in the human testis extract. The NZ-3 antigen was located on the acrosomal and tail regions of human sperm cell and the NZ-3 Ab significantly (P < 0.001) inhibited human sperm capacitation and/or acrosome reaction. The novel recombinant NZ-3 antigen may find applications in immunocontraception and in specific diagnosis of human infertility.

Amino Acid Sequence↗
PubMed1996

Functional interaction between release factor one and P-site peptidyl-tRNA on the ribosome.

Translation termination at UAG is influenced by the nature of the 5' flanking codon in Escherichia coli. Readthrough of the stop codon is always higher in a strain with mutant (prfA1) as compared to wild-type (prfA+) release factor one (RF1). Isocodons, which differ in the last base and are decoded by the same tRNA species, affect termination at UAG differently in strains with mutant or wild-type RF1. No general preference of the last codon base to favour readthrough or termination can be found. The data suggest that RF1 is sensitive to the nature of the wobble base anticodon-codon interaction at the ribosomal peptidyl-tRNA binding site (P-site). For some isoaccepting P-site tRNAs (tRNA3(Pro) versus tRNA2(Pro), tRNA4(Thr) versus tRNA1,3Thr) the effect is different on mutant and wild-type RF1, suggesting an interaction between RF1 at the aminoacyl-tRNA acceptor site (A-site) and the P-site tRNA itself. The glycine codons GGA (tRNA2(Gly)) and GGG (tRNA2,3(Gly)) at the ribosomal P-site are associated with an almost threefold higher readthrough of UAG than any of the other 42 codons tested, including the glycine codons GGU/C, in a strain with wild-type RF1. This differential response to the glycine codons is lost in the strain with the mutant form of RF1 since readthrough is increased to a similar high level for all four glycine codons. High alpha-helix propensity of the last amino acid residue at the C-terminal end of the nascent peptide is correlated with an increased termination at UAG. The effect is stronger on mutant compared to wild-type RF1. The data suggest that RF1-mediated termination at UAG is sensitive to the nature of the codon-anticodon interaction of the wobble base, the last amino acid residue of the nascent peptide chain, and the tRNA at the ribosomal P-site.

Amino Acids↗
PubMed2000

An unexpected affected female patient in a classical Lesch-Nyhan family.

Lesch-Nyhan disease is a genetic disorder of purine metabolism caused by defective activity of the enzyme hypoxanthine-guanine phosphoribosyl transferase (HPRT), resulting from mutation in the corresponding gene on the long arm of the X chromosome (Xq26). The classical phenotype, which includes spasticity, involuntary movements, developmental disability, and self-injurious behavior, occurs exclusively in males, while heterozygous, carrier females are clinically normal. We analyzed an Argentine family in which there were male and female siblings with clinically identical classic features of Lesch-Nyhan disease. The mother and an older daughter were carriers and had normal phenotypes. We identified the HPRT mutation in the family. It is a C --> T transition at position 508 of the cDNA (c.508 C --> T) that changes the CGA codon for Arg(169) to the TGA stop codon (R169X). The female patient was karyotypically normal and heterozygous for the mutation. She inherited the HPRT mutation from her mother, but she also had unexpected nonrandom inactivation of the paternal X chromosome carrying the normal HPRT gene. This additional genetic alteration is the cause of the clinical expression of disease in this female patient.

Adult↗
PubMed1995

A procedure for the generation and the purification of Escherichia coli thioredoxins with variable N-terminal sequences.

We have developed a rapid and simple procedure for the production and the purification of Escherichia coli thioredoxins containing additional amino acid residues at the N-terminus. By the polymerase chain reaction, the complete gene encoding for E. coli thioredoxin was modified and amplified with the addition at its 5' end of a BamHI cloning site and a triplet coding for an arginine residue instead of the initiator methionine codon, whereas at the 3' end the stop codon was followed by an EcoRI cloning site. The synthetic DNA was ligated into the BamHI/EcoRI site of the vector plasmid pGEX-2T, and the novel plasmid [pFTG] was used for the transformation of E. coli cells. Following induction and cell disruption, a protein composed of Schistosoma japonicum glutathione S-transferase and E. coli thioredoxin was obtained in soluble form and purified by affinity chromatography on agarose columns bearing immobilized glutathione. This procedure yielded 50 mg of homogeneous fusion protein per liter of culture media. Digestion of the chimeric thioredoxin with bovine plasma thrombin followed by an additional chromatography on glutathione-agarose gave a protein that contained the entire sequence of E. coli thioredoxin and three additional amino acid residues [G-S-R-] at the N-terminal side. The structural characteristics and the protein disulfide oxidoreductase activity of this recombinant protein, in terms of variations of emission fluorescence and reduction of insulin disulfide bonds, respectively, were essentially identical to those of its counterpart obtained from wild-type cells by conventional techniques of proteins purification.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1996

Phenylalanine ammonia-lyase gene structure, expression, and evolution in Nicotiana.

Phenylalanine ammonia-lyase (PAL) catalyzes the first reaction in the general phenylpropanoid pathway leading to the production of phenolic compounds with a significant range of biological function. A PAL gene we designated gPAL1, cloned from tobacco, consists of two exons separated by an intron of 1932 bp. Exon I, 398 bp, and exon II, 1747 bp, together encode a polypeptide of 715 amino acids. A putative TATA box and polyadenylation signal are found 144 bp upstream of the initiation codon and 193 bp downstream from the stop codon, respectively. Using various parts of gPAL1 as probes, genomic Southern blots indicated the presence of a small family of PAL genes in the tobacco genome that can be divided into two distinct subfamilies, one consisting of pal1 and pal2 and another of pal3 and pal4. Comparative genomic blot analysis of progenitor species (Nicotiana tomentosiformis and N. sylvestris) indicated that each species contains one PAL gene from each of the subfamilies, suggesting that pal1 and pal3 (or pal2 and pal4) diverged prior to the evolution of N. tabacum. Expression of the PAL gene family was examined using RNA gel blots. PAL transcript levels were significantly higher in flowers and roots than in leaves and stems of mature plants. PAL transcripts accumulate differentially during flower and leaf maturation in that mRNA levels decline during flower maturation but increase during leaf maturation. In leaves, PAL transcripts rapidly accumulated afer wounding.

Amino Acid Sequence↗
PubMed1993

The six genes of the Rubisco small subunit multigene family from Mesembryanthemum crystallinum, a facultative CAM plant.

The nucleotide sequences of the entire gene family, comprising six genes, that encodes the Rubisco small subunit (rbcS) multigene family in Mesembryanthemum crystallinum (common ice plant), were determined. Five of the genes are arranged in a tandem array spanning 20 kb, while the sixth gene is not closely linked to this array. The mature small subunit coding regions are highly conserved and encode four distinct polypeptides of equal lengths with up to five amino acid differences distinguishing individual genes. The transit peptide coding regions are more divergent in both amino acid sequence and length, encoding five distinct peptide sequences that range from 55 to 61 amino acids in length. Each of the genes has two introns located at conserved sites within the mature peptide-coding regions. The first introns are diverse in sequence and length ranging from 122 bp to 1092 bp. Five of the six second introns are highly conserved in sequence and length. Two genes, rbcS-4 and rbcS-5, are identical at the nucleotide level starting from 121 bp upstream of the ATG initiation codon to 9 bp downstream of the stop codon including the sequences of both introns, indicating recent gene duplication and/or gene conversion. Functionally important regulatory elements identified in rbcS promoters of other species are absent from the upstream regions of all but one of the ice plant rbcS genes. Relative expression levels were determined for the rbcS genes and indicate that they are differentially expressed in leaves.

Adaptation, Biological↗
PubMed1997

AFX1 and p54nrb: fine mapping, genomic structure, and exclusion as candidate genes of X-linked dystonia parkinsonism.

We have mapped AFX1 and p54nrb to a yeast artificial chromosome (YAC) contig of Xq13.1 that harbors the X-linked dystonia parkinsonism (XDP) locus DYT3. AFX1 is flanked by loci DXS7116 and Il2R gamma, and p54nrb by loci DXS6673E and DXS7120. The exon-intron structure of both genes was analyzed. AFX1 is composed of three exons with most of exon 3 being untraslated. p54nrb is made up of 12 exons ranging in size from 40 bp to 1227 bp. The start codon is in exon 3 and the stop codon in exon 12. Both genes are expressed in the brain, among other tissues. AFX1 and p54nrb were excluded as candidates of DYT3 by sequencing of the exons and the flanking intronic sequences in an XDP patient and a control, and by Northern blot analysis.

Animals↗
PubMed1990

Chronic active hepatitis with hepatitis B virus DNA and antibody against e antigen in the serum. Disturbed synthesis and secretion of e antigen from hepatocytes due to a point mutation in the precore region.

Some patients with type B chronic active hepatitis have a high titer of hepatitis B virus DNA despite antibody against e antigen in the serum. Clones of hepatitis B virus were propagated from the sera of seven patients with this disease, and the precore region was sequenced. Essentially all clones (128/131 or 98%) showed a point mutation from guanine to adenine at nucleotide 83, converting codon 28 for tryptophan (TGG) to a stop codon (TAG); the second guanine-to-adenine point mutation at nucleotide 86 was identified in only 29 clones from two patients. In patients followed up since they had hepatitis B e antigen, a shift from guanine to adenine was observed at nucleotide 83 along with the seroconversion to the antibody to e antigen. The precore-region product is required for the synthesis and secretion of e antigen from hepatocytes. A point mutation from guanine to adenine at nucleotide 83 observed in the seven patients, therefore, would be responsible for disturbed secretion of e antigen.

Aged↗
PubMed1991

Fulminant hepatitis B: induction by hepatitis B virus mutants defective in the precore region and incapable of encoding e antigen.

Clones of hepatitis B virus were propagated from 10 cases of fulminant hepatitis B after amplification by polymerase chain reaction and their nucleotide sequences of the precore region were determined. All 113 clones from 9 cases had a point mutation from guanine to adenine at nucleotide 83 in the precore region, which converted codon 28 for tryptophan (TGG) to a stop codon (TAG) and prohibited the synthesis and secretion of hepatitis B e antigen. Precore-region defects were not detected in any of 23 clones from the remaining 1 case. By contrast, precore-region defects were not found in any of 180 clones from 8 cases of acute hepatitis B without hepatic failure serving as controls. The source of infection was traceable in 3 cases. The same precore-region defect, along with the sequence identity of 435 nucleotides, was observed in clones from the case of a baby and his grandmother, who carried the virus and was implicated in the transmission, and also in clones from two pediatricians and the carrier patients they attended. These findings support the hypothesis that precore-defective mutants have stronger activity to induce fulminant hepatitis than nondefective viruses.

Adolescent↗
PubMed1991

Molecular analysis of the gene 6 from a porcine group C rotavirus that encodes the NS34 equivalent of group A rotaviruses.

The complete nucleotide sequence of the gene 6 from the porcine group (Gp) C rotavirus strain Cowden was determined from gene 6-specific clones selected from a cDNA library and from viral transcript RNA. The gene is 1348 nucleotides in length with a potential initiation codon beginning at nucleotide 25 and a stop codon at nucleotide 1231. The deduced protein contains 402 amino acids. Comparison of the gene 6 from this Gp C strain with sequences in the GenBank data base indicated that this gene shared homology with gene 7 of Gp A rotavirus strain SA-11 (22.9%) and gene 9 of Gp A rotavirus strain UK (22.6%), both of which encode the NS34 protein. In vitro translation products produced from transcripts generated from a gene 6 clone containing the entire open reading frame were not immunoprecipitated with either hyperimmune serum specific for the Gp C Cowden strain or a monoclonal antibody directed against the group antigen (VP6) of the Cowden strain. However, products generated from a full-length gene 5 clone of the Cowden strain were immunoprecipitated by each of these antibodies. These data suggest that in contrast to the Gp A viruses in which the gene 6 encodes the major inner capsid protein VP6, the gene 6 of the Cowden Gp C strain encodes a nonstructural protein corresponding to the NS34 of Gp A rotaviruses.

Amino Acid Sequence↗
PubMed1992

Dugbe Nairovirus M RNA: nucleotide sequence and coding strategy.

The coding assignments of the medium-sized (M) RNA segment of the Dugbe (DUG) virus (Nairovirus, Bunyaviridae) were investigated. The complete nucleotide sequence of 4888 nucleotides (nt) contained one long open reading frame in the viral complementary RNA, extending from an AUG start codon at nt 48-50 to a stop codon at nt 4701-4703 (numbered from the 5' terminus of vcRNA). Comparison of the terminal sequences with the ends of the DUG S segment revealed sequence identity between the first nine nucleotides of both segments. No sequence homologies were found with the M segments of other members of the Bunyaviridae, or with their polypeptide products. Expression of portions of the DUG M open reading frame in Escherichia coli demonstrated the carboxyl terminal region of the M open reading frame codes for the G1 structural glycoprotein, which is the target for neutralising antibodies. Confirmation of this assignment was obtained by sequencing the amino terminus of the G1 protein. Two nonstructural glycoproteins which share epitopes with G1 were identified in virus-infected cells, one of which (85 kDa) is processed over a period of several hours to produce G1. The G2 coding region was located upstream of the G1 sequence. The region between the carboxyl terminus of G2 and the 5' end of the long open reading frame apparently encodes a nonstructural protein of about 70 kDa, which is a precursor of the G2 protein.

Amino Acid Sequence↗
PubMed1989

Sequence analysis of the Clostridium cellulolyticum endoglucanase-A-encoding gene, celCCA.

The nucleotide sequence of a Clostridium cellulolyticum endo-beta-1,4- glucanase (EGCCA)-encoding gene (celCCA) and its flanking regions, was determined. An open reading frame (ORF) of 1425 bp was found, encoding a protein of 475 amino acids (aa). This ORF began with an ATG start codon and ended with a TAA ochre stop codon. The N-terminal region of the EGCCA protein resembled a typical signal sequence of a Gram-positive bacterial extracellular protein. A putative signal peptidase cleavage site was determined. EGCCA, without a signal peptide, was found to be composed of more than 35% hydrophobic aa and to have an Mr of 50715. Comparison of the encoded sequence with other known cellulase sequences showed the existence of various kinds of aa sequence homologies. First, a strong homology was found between the C-terminal region of EGCCA, containing a reiterated stretch of 24 aa, and the conserved reiterated region previously found to exist in four Clostridium thermocellum endoglucanases and one xylanase from the same organism. This region was suspected of playing a role in organizing the cellulosome complex. Second, an extensive homology was found between EGCCA and the N-terminal region of the large endoglucanase, EGE, from C. thermocellum, which suggests that they may have a common ancestral gene. Third, a region, which extended for 21 aa residues beginning at aa + 127, was found to be homologous with regions of cellulases belonging to Bacilli, Clostridia and Erwinia chrysanthemi.

Amino Acid Sequence↗
PubMed1995

Functional domains of the C-terminus of the rat angiotensin AT1A receptor.

Previous work has shown that truncating the carboxyl terminus (C-terminus) of the rat angiotensin AT1A receptor to 309 amino acids abolished G-protein coupling and receptor internalization. This suggests that domains responsible for these functions lie beyond amino acid 309 of the C-terminus. The objective of this study was to determine the effect on angiotensin AT1A receptor function and regulation of deleting 41 amino acids from the C-terminus, which include the putative protein kinase C phosphorylation sites. Using site directed mutagenesis, the codon for Tyr319 was converted to a stop codon and the resulting truncated receptor permanently expressed in cultured human kidney cells. The properties of the truncated receptor were compared to those of the full length receptor. Expression of the truncated receptor was confirmed by sodium dodecyl sulphate polyacrylamide gel electrophoresis analysis of photolabelled membrane preparations. Angiotensin II activation of both full length and truncated receptors resulted in mobilization of inositol phosphates. However, whereas this was associated with rapid internalization of the full length receptor, the truncated receptor failed to internalize. Furthermore, pretreatment of cells with phorbol 12-myristate 13-acetate, a direct activator of protein kinase C, markedly attenuated the full length, but no the truncated receptor's ability to mobilise inositol phosphates. Thus, we conclude that the domain between amino acids 309 & 318 is important for G-protein coupling; that amino acids beyond 318 regulate internalization and one or more of the putative protein kinase C phosphorylation sites, present in the C-terminus of the angiotensin At1A receptor, actively regulate the receptor.

Angiotensin II↗
PubMed2005

Analbuminemia in a Swiss family is caused by a C --> T transition at nucleotide 4446 of the albumin gene.

OBJECTIVE: To define the molecular defect that causes analbuminemia in an apparently healthy boy, son of non-consanguineous Swiss parents. DESIGN AND METHODS: Total DNA, extracted from peripheral blood samples from the proband and from both parents, was PCR-amplified using oligonucleotide primers designed to amplify the 14 exons of the human albumin gene and the flanking intron regions. The products were screened for mutations by single-strand conformation polymorphism (SSCP) and heteroduplex analyses (HA) either directly or after digestion with restriction enzymes. The combination of these methods identified the abnormal fragment, which was then sequenced. RESULTS: DNA sequence analysis identified in the homozygous proband a C --> T transition at nucleotide 4446. The mutation changes the codon CGA for Arg 114 to a stop codon TGA, resulting in premature termination and is therefore responsible for the analbuminemic trait. The same mutation has been previously reported to cause analbuminemia in an American female. The putative protein product would have a length of 113 residues. The parents were found to be heterozygous for the mutation. CONCLUSIONS: Gel-based mutation detection and DNA sequencing confirmed the diagnosis of congenital analbuminemia in the proband. Our results show that the combination of SSCP and HA represents a powerful tool to study the molecular defects causing analbuminemia in humans.

Albumins↗
PubMed2006

Nonsense mutation of feline beta-hexosaminidase beta-subunit (HEXB) gene causing Sandhoff disease in a family of Japanese domestic cats.

G(M2) gangliosidoses are inherited metabolic disorders and are caused by severely reduced enzymatic activity of lysosomal beta-hexosaminidase. In the present study, the open reading frame (ORF) of the HEXB gene in a family of Japanese domestic cats with G(M2) gangliosidosis variant 0 (Sandhoff disease) was determined. Two types of abnormal cDNA clones were obtained from the liver of an affected cat tissue. One showed a single nucleotide substitution from C to T at nucleotide position 667 of the HEXB ORF. In the deduced amino acid sequence, the codon of arginine was altered to a stop codon. The genotyping, using PCR-primer introduced restriction analysis confirmed that Sandhoff disease in this family is associated with this nonsense mutation. Discovery of the nonsense mutation will permit the confirmation of the clinical diagnosis of Sandhoff disease in conjugation with the already established enzyme-based test.

Animals↗
PubMed2000

Silent polymorphisms within the coding region of human sodium/hydrogen exchanger isoform-1 cDNA in peripheral blood mononuclear cells of leukemia patients: A comparison with healthy controls.

We have examined the sequence of the cDNA encoding the sodium/hydrogen exchanger isoform 1 (NHE1), from 23 bases upstream of the start codon to 28 bases downstream of the stop codon. Template was prepared from (1) peripheral blood mononuclear cells (PBMC) isolated from 10 healthy unrelated Caucasian volunteers; (2) PBMCs isolated from 6 leukemic patients (acute lymphoblastic leukemia [ALL], n = 3; chronic lymphocytic leukemia [CLL], n = 1; chronic myelogenous leukemia [CML], n = 2); and (3) samples of 4 leukemic cell lines (ALL: CEM, MOLT4; AML: KG1a; CML: K562). NHE1 cDNA in normal PBMCs showed silent polymorphism of nucleotides 112 (N1: T, frequency 0.70; C, frequency 0.30; prevalence of heterozygosity 0.42); 2248 (N2: G, frequency 0.90; A, frequency 0. 10; heterozygosity 0.18); and 2493 (N3: G, frequency 0.90; A, frequency 0.10; heterozygosity 0.18). Deduced primary structure of NHE1 protein in all normal volunteers was identical to that previously published for NHE1 from renal and cardiac tissue. Similar to normal PBMCs, NHE1 cDNA from leukemic cells showed polymorphism of nucleotides N1, N2, and N3, but failed to demonstrate leukemia-specific sequence differences. We conclude that the coding region of NHE1 cDNA shows a greater level of polymorphism than is currently recognized, but that sequence mutation of NHE1 is not a key event in the pathogenesis of leukemia.

Adult↗