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A frame-shift mutation of the androgen receptor gene in a patient with receptor-negative complete testicular feminization: comparison with a single base substitution in a receptor-reduced incomplete form.

Mutations of the androgen receptor that impair the action of androgens result in abnormal male sexual development. We studied the structure of the androgen receptor gene in a patient with the receptor-negative form of complete testicular feminization and another patient with a receptor-reduced form of incomplete testicular feminization. In the subject with complete testicular feminization, the deletion of a single nucleotide occurred at nucleotide number 1893 at exon 2. The subsequent frame-shift mutation changes the sense of codon 622 from cysteine to a translational stop signal. Codon 622 is exon 3, so the mutation predicts the synthesis of a truncated receptor that lacks the entire androgen-binding domain. Analysis of a subject with incomplete testicular feminization revealed a single substitution (CGT --> CAT) at nucleotide 2675 of exon 7, resulting in the conversion of an arginine at amino acid 840 to a histidine. This mutation in the androgen-binding domain may impair, but not remove, the androgen binding to its receptor. These results suggest that the phenotypes in our subjects are due to the mutations, and that single amino acid substitution and premature termination codon can cause variably severe functional abnormalities.

Adult↗

A molecular framework for the phylogeny of the ant subfamily dolichoderinae.

Partial sequences are reported for the mitochondrial genes for cytochrome oxidase subunits 2 and 3 and for cytochrome b, and the entire sequence of the gene for tRNA(Leu)(UUR) for species from 14 genera of dolichoderine ants and from three outgroup genera. Considerable variation was observed between tRNA genes in the size of the TPsiC arm and the DHU and anticodon loops and whether or not the TPsiC stem possesses a GC pair. The outgroup taxa showed complete TAA CO1 stop codons, but dolichoderines have either TA or T. The outgroup taxa showed a noncoding gap between the CO1 and the tRNA(Leu)(UUR) genes. A phylogeny-independent compatibility test using the amino acid sequences showed differences between the genes consistent with variation in evolutionary rates, according with other studies. Base compositions proved heterogeneous between species, hence phylogenetic analysis was restricted to the protein sequences using maximum likelihood and the mtREV24 replacement matrix. A maximum-likelihood consensus tree has similarities to those from morphological studies with some exceptions such Leptomyrmex falling within the dolichoderine genera rather than basally, and the accretion of genera formerly included under Iridomyrmex. Features of the tRNA genes and the CO1 termination codons agree quite well with the molecular phylogeny.

Animals↗

The association of nonsense codons with exon skipping.

Some genes that contain premature nonsense codons express alternatively-spliced mRNA that has skipped the exon containing the nonsense codon. This paradoxical association of translation signals (nonsense codons) and RNA splicing has inspired numerous explanations. The first is based on the fact that premature nonsense codons often reduce mRNA abundance. The reduction in abundance of full-length mRNA then allows more efficient amplification during PCR of normal, minor, exon-deleted products. This mechanism has been demonstrated to explain an extensive correlation between nonsense codons and exon-skipping for the hamster Hprt gene. The second explanation is that the mutation producing an in-frame nonsense codon has an effect on exon definition. This has been demonstrated for the Mup and hamster Hprt gene by virtue of the fact that missense mutations at the same sites also are associated with the same exon-deleted mRNA. The third general explanation is that a hypothetical process takes place in the nucleus that recognizes nonsense codons, termed 'nuclear scanning', which then has an effect on mRNA splicing. Definitive evidence for nuclear scanning is lacking. My analysis of both nonsense and missense mutations associated with exon skipping in a large number of genes revealed that both types of mutations frequently introduce a T into a purine-rich DNA sequence and are often within 30 base pairs of the nearest exon boundary. This is intriguing given that purine-rich splicing enhancers are known to be inhibited by the introduction of a T. Almost all mutations associated with exon skipping occur in purine-rich or A/C-rich sequences, also characteristics of splicing enhancers. I conclude that most cases of exon skipping associated with premature termination codons may be adequately explained either by a structural effect on exon definition or by nonquantitative methods to measure mRNA, rather than an effect on a putative nuclear scanning mechanism.

Animals↗

The destabilization of IL-2 mRNA by a premature stop codon and its differential stabilization by trans-acting inhibitors of protein synthesis do not support a role for active translation in mRNA stability.

To investigate the role that translation plays in the stabilization of the IL-2 mRNA, we inhibited protein synthesis in both cis and trans. To block translation in trans, we utilized the inhibitors puromycin (PUR) and cycloheximide (CHX), which differentially effect polysome structure. We found that CHX enhances the stability of IL-2 mRNA in cells stimulated with anti-TCR Ab alone, but it inhibits CD28-induced message stabilization in costimulated cells. In contrast, PUR had a minimal effect on IL-2 mRNA stability in either the presence or absence of costimulation. The differential effects of these two inhibitors suggest that: 1) CHX is unlikely to stabilize the IL-2 mRNA by inhibiting the expression of a labile RNase; 2) CD28-mediated IL-2 mRNA stabilization does not require translation; and 3) IL-2 mRNA decay is not coupled to translation. To block translation in cis, we generated sequence-tagged IL-2 genomic reporters that contain a premature termination codon (PTC). In both the presence and absence of costimulation, these PTC-containing mRNAs exhibit drastically diminished stability. Interestingly, the addition of CHX but not PUR completely restored CD28-mediated stabilization, suggesting that CHX can block the enhanced decay induced by a PTC. Finally, CHX was able to superinduce IL-2 mRNA levels in anti-TCR Ab-stimulated cells but not in CD28-costimulated cells, suggesting that CHX may also act by other mechanisms.

Animals↗

Reexamination of the sequence of the sea urchin egg receptor for sperm: implications with respect to its properties.

A reexamination of the cDNA clones of the Strongylocentrotus purpuratus sea urchin egg receptor for sperm resulted in several important changes to the sequence. By using both rapid amplification of cDNA ends (RACE) and Northern blot analysis for confirmation, the corrected deduced amino acid sequence was shown to lack a classical signal peptide. In addition, a frame shift resulted in a stop codon terminating the deduced sequence prior to a putative transmembrane domain, thereby truncating the protein to 889 amino acids. The deduced amino acid sequence of the receptor has high sequence similarity to the hsp 110 subfamily of proteins. These findings on the primary structure of the egg receptor for sperm raise important questions concerning the mechanism by which the heavily glycosylated receptor is localized to the extracellular surface of the egg and to the cortical granules.

Amino Acid Sequence↗

Pharmacologic therapy for stop mutations: how much CFTR activity is enough?

PURPOSE OF REVIEW: The purpose of this review is to summarize the recent approaches using mutation-specific therapy to correct the genetic defect according to the molecular mechanism by which the mutation causes the defects in cystic fibrosis transmembrane conductance regulator (CFTR). Premature stop mutations (class I mutations) account for 5 to 10% of the total mutant alleles in cystic fibrosis patients, and in certain subpopulations the incidence is much higher. RECENT FINDINGS: The aminoglycoside antibiotics can suppress premature termination codons by permitting translation to continue to the normal termination of the transcript. The susceptibility to suppression by aminoglycosides depends on the stop codon itself and on the sequence context surrounding it. In vitro studies in cell lines expressing stop mutations and in mice have shown that aminoglycosides caused a dose-dependent increase in CFTR expression and restored functional CFTR to the apical membrane. Clinical studies also provided evidence that the aminoglycoside gentamicin can suppress these CFTR premature stop mutations in affected patients. A recent double-blind, placebo-controlled, crossover study has demonstrated restoration of CFTR function by topical application of gentamicin to the nasal epithelium of cystic fibrosis patients carrying stop mutations. In 21% of the patients there was a complete normalization of all the electrophysiologic abnormalities caused by the CFTR defect, and in 68% there was restoration of either chloride or sodium transport. Furthermore, immunohistochemical staining to the C-terminal part of the CFTR was demonstrated via peripheral staining for CFTR in scraped nasal epithelial cells of patients carrying stop mutations. Inconsistent results were reported regarding the required level of corrected CFTR that has to be reached to achieve normal function. Achieving CFTR activity of 10 to 35% might be needed to prevent significant pulmonary morbidity. SUMMARY: It is as yet unknown how much corrected mutant CFTR must reach the apical membrane to induce a clinically relevant beneficial effect. The future goal is to maximize the effect of stop-codon supressors on CFTR while minimizing side effects, but further studies must be performed to find a safer compound that may be administered in small children from the time of diagnosis.

Aminoglycosides↗

A-2-->G transition at the 3' acceptor splice site of IVS17 characterizes the COL2A1 gene mutation in the original Stickler syndrome kindred.

Hereditary progressive arthro-ophthalmopathy, or "Stickler syndrome," is an autosomal dominant osteochondrodysplasia characterized by a variety of ocular and skeletal anomalies which frequently lead to retinal detachment and precocious osteoarthritis. A variety of mutations in the COL2A1 gene have been identified in "Stickler" families; in most cases studied thus far, the consequence of mutation is the premature generation of a stop codon. We report here the characterization of a COL2A1 gene mutation in the original kindred described by Stickler et al. [1965]. Conformational sensitive gel electrophoresis (CSGE) [Ganguly et al., 1993] was used to screen for mutations in the entire COL2A1 gene in an affected member from the kindred. A prominent heteroduplex species was noted in the polymerase chain reaction (PCR) product from a region of the gene including exons 17 to 20. Direct sequencing of PCR-amplified genomic DNA resulted in the identification of a base substitution at the A-2 position of the 3' splice acceptor site of IVS17. Sequencing of DNA from affected and unaffected family members confirmed that the mutation segregated with the disease phenotype. Reverse transcriptase-PCR analysis of poly A+ RNA demonstrated that the mutant allele utilized a cryptic splice site in exon 18 of the gene, eliminating 16 bp at the start of exon 18. This frameshift eventually results in a premature termination codon. These findings are the first report of a splice site mutation in classical Stickler syndrome and they provide a satisfying historical context in which to view COL2A1 mutations in this dysplasia.

Adolescent↗

Precursor RNAs harboring nonsense codons accumulate near the site of transcription.

Messenger RNAs containing premature termination codons (PTCs) are selectively eliminated by nonsense-mediated mRNA decay (NMD). Paradoxically, although cytoplasmic ribosomes are the only known species capable of PTC recognition, in mammals many PTC-containing mRNAs are apparently eliminated prior to release from the nucleus. To determine whether PTCs can influence events within the nucleus proper, we studied the immunoglobulin (Ig)-mu and T cell receptor (TCR)-beta genes using fluorescent in situ hybridization (FISH). Alleles containing PTCs, but not those containing a missense mutation or a frameshift followed by frame-correcting mutations, exhibited elevated levels of pre-mRNA, which accumulated at or near the site of transcription. Our data indicate that mRNA reading frame can influence events at or near the site of gene transcription.

Animals↗

UGA suppression by normal tRNA Trp in Escherichia coli: codon context effects.

The nucleotide sequences at the 3' side of in-phase UGA termination codons in mRNAs of various prokaryotic genes were re-examined. An adenine (A) residue is found to be adjacent to the 3' side of UGA in mRNAs which code for readthrough proteins by the suppression of UGA by normal Escherichia coli tRNA Trp. It is suggested that the nature of the nucleotide following a UGA codon determines whether the UGA signals inefficiently or efficiently the termination of polypeptide chain synthesis: an A residue at this position permits the UGA readthrough process.

Base Sequence↗

Translational regulation of myelin basic protein synthesis.

Synthesis of the mouse myelin basic proteins (MBPs) was studied in reticulocyte lysates programmed with brain mRNA in the presence or absence of brain factors. Addition of brain factors to the lysates increased the incorporation of [35S]methionine into total TCA-precipitable protein by a factor of 6-9, and the majority of this stimulation was found to be due to initiation factors. Although brain factors increased total protein synthesis, the percentage of MBP synthesis was reduced from 4.3% of the total counts incorporated (in the absence of brain factors) to 1.4% (in their presence). Increasing the concentration of brain mRNA in the lysates also reduced the relative levels of MBP synthesis. These results suggested the MBP mRNAs, as a group, were less efficiently initiated than most brain mRNAs. An analysis of the nucleotide sequence flanking the initiator codon of the MBP mRNAs indicates the presence of a second AUG codon 5 bases upstream, immediately followed by a termination codon, which may provide a structural explanation for the poorer initiation efficiency of the MBP mRNAs. Further analysis of the synthesis of the individual MBPs in the presence or absence of inhibitors of initiation (7-methylguanosine triphosphate and aurintricarboxylic acid) and elongation (anisomycin and emetine) indicated than the 14-kD MBP mRNA was less efficiently translated than the other MBP mRNAs. Synthesis of the 14-kD MBP was more strongly inhibited by the initiation inhibitors than the other MBP mRNAs, and synthesis of the 14-kD MBP was increased relative to the other MBPs in the presence of elongation inhibitors.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

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↗

Analysis of barley nitrate reductase cDNA and genomic clones.

Barley nitrate reductase cDNA and genomic clones were isolated by homology with the barley nitrate reductase cDNA clone bNRp10 and sequenced. This is the first reported analysis of a full-length nitrate reductase gene and its corresponding cDNA in the same species. The longest cDNA clone extends to within 9 bp of the ATG start codon and the sequence is similar to that reported for the higher plant NR sequences. As expected, the amino acid sequence of barley nitrate reductase is more related closely to the rice (84% homology) than to the Arabidopsis (62%) sequence. Four different polyA addition sites were identified from sequence analysis of nine barley NR cDNA clones. A 7.3 kb region of a genomic recombinant lambda clone was subcloned as two contiguous BamHI fragments into p Bluescript, designated pMJ7 and pMJ8, and sequenced. These clones include the entire nitrate reductase coding region, one large intron, 2.7 kb of untranslated sequence 5' to the translation start codon and 0.25 kb 3' to the translation termination codon. The mRNA cap site was identified as a cytosine, 111 bases upstream of the ATG translation start codon. The putative CAAT and TATA boxes were identified at -115 and -33 bp, respectively, with the mRNA cap site designated as +1. The barley nitrate reductase gene coding region strongly favors G or C in the third codon position.

Base Sequence↗

Beta2-microglobulin gene mutation is not a common mechanism of HLA class I total loss in human tumors.

One hundred and sixty-two tumor samples were analyzed for HLA class I expression using immunohistological techniques. HLA class I total loss (phenotype no. I) was detected in 31 cases (19%), comprising 20 colorectal, 3 laryngeal, and 2 bladder carcinomas and 6 melanomas. Twenty-one cases were selected for molecular analysis due to a higher proportion of tumor cells versus stroma cells (75%). We investigated whether beta2-microglobulin mutation was responsible for HLA downregulation. Single-strand conformation polymorphism and sequencing analysis of DNA samples was performed. Alterations were detected only in melanomas M78 (a point mutation in the initiation ATG sequence), M79 (a mutation in codon 31 producing a stop codon), and M34 (a TTCT deletion introducing a termination codon signal). We found no beta2-microglobulin gene mutation in the other 18 samples. Loss of heterozygosity in 15q close to the beta2-microglobulin gene was found in 5 cases. We conclude that HLA class I total loss can frequently occur without beta2-microglobulin gene mutations.

Colorectal Neoplasms↗

A point mutation in exon 7 of the C1-inhibitor gene causing type I hereditary angioedema.

The polymerase chain reaction and nucleotide sequence analysis have been used to characterize a point mutation in the seventh exon of one allele of the C1-inhibitor gene in a family with type I hereditary angioedema. A single base change (C-->T) at nucleotide 1482 in C1-inhibitor converted the codon for Gln-339 to a premature translation termination codon, TAG. Family studies suggest that this mutation is responsible for type I hereditary angioedema in a studied pedigree.

Amino Acid Sequence↗

UGA nonsense mutation in the alcohol dehydrogenase gene of Drosophila melanogaster.

A mutant gene, which we have designated AdhnB, codes for a defective form of the enzyme alcohol dehydrogenase in Drosophila melanogaster. We show that the polypeptide encoded by AdhnB is approximately 2000 Mr smaller than the protein synthesized under the direction of the wild-type alcohol dehydrogenase gene. In contrast, the alcohol dehydrogenase mRNA produced by both genes is the same size. We cloned and sequenced a portion of the protein-coding region of AdhnB and compared it to the same region in the wild-type gene. We found a single base substitution: a change of the TGG tryptophan codon at amino acid 235 to a TGA termination codon. This nonsense mutation accounts for the observed reduction in size of the alcohol dehydrogenase polypeptide. In further studies, we found that the steady-state levels of alcohol dehydrogenase mRNA in flies carrying the AdhnB gene and the wild-type alcohol dehydrogenase gene were indistinguishable. However, the steady-state level of alcohol dehydrogenase polypeptide was reduced to 1% of wild-type levels in flies with the AdhnB gene. Moreover, the rate of alcohol dehydrogenase synthesis in mutant flies was reduced to 50% of that found in wild type. The aberration in AdhnB thus affects both the rate of synthesis and the rate of degradation of the alcohol dehydrogenase peptide. AdhnB is the first reported nonsense mutant in Drosophila.

Alcohol Oxidoreductases↗

The structure of the human zeta-globin gene and a closely linked, nearly identical pseudogene.

DNA sequencing studies indicate that only one of two closely linked human embryonic alpha-like globin genes, zeta (zeta), encodes a functional polypeptide. The other is a pseudogene (psi zeta) that differs by only 3 bp in the protein coding sequence, one of which converts the codon for amino acid 6 into a chain termination codon. Both zeta-globin genes differ from all other alpha-like genes thus far reported in that they contain large introns consisting, in part, of simple repeat sequences. Intron 1 of each gene contains a variation of the repeat sequence ACAGTGGGGAGGGG, while intron 2 contains the repeat sequence CGGGG. Comparison of the human zeta- and alpha-globin gene sequences reveals that the embryonic and adult alpha-like genes began to diverge from each other relatively early in vertebrate evolution (400 million years ago). In contrast, the beta-like embryonic globin gene, epsilon (epsilon), is the product of a much more recent evolutionary event (200 million years ago). Thus, even though the temporal and quantitative expression of zeta- and epsilon-globin genes must be coordinately controlled during development, their evolutionary histories are clearly distinct.

Amino Acid Sequence↗

Subcellular localization of the MEN, MLL/MEN and truncated MLL proteins expressed in leukemic cells carrying the t(11;19)(q23;p13.1) translocation.

The t(11;19)(q23;p13.1) translocation is exclusively associated with myeloid leukemias. Previously, we cloned several species of MLL/MEN chimeric cDNAs in a patient with myeloid leukemia carrying the t(11;19)(q23;p13.1) translocation. The MEN sequence directly followed the 5' region of MLL cDNA in some species and otherwise there presented an inserted sequence of 120 bp between the MLL and MEN sequences in others. Because the insertion sequence contained an in-frame termination codon, they coded only for the NH2-terminal part of MLL (truncated MLL). We also cloned the normal MEN cDNA in full-length with a cDNA library derived from K562 cells. We expressed the normal MEN, MLL/MEN chimeric and truncated MLL proteins in COS7 cells with the corresponding cDNAs and detected them with antibodies raised against the MEN and MLL peptides. Immunostaining and subcellular fractionation showed nuclear localization of all these proteins. These findings suggested that MLL/MEN chimeric cDNAs were actually translated into both MLL/MEN fusion and truncated MLL proteins and that they were localized in the nucleus of leukemic cells. Recently, Conaway et al. reported that MEN is an RNA polymerase II elongation factor. The leukemogenesis by the t(11;19)(q23;p13.1) translocation may have resulted from the alteration of transcription regulation induced by the MLL/MEN fusion protein and/or the truncated MLL protein.

Animals↗

Pseudodominance of lipoprotein lipase (LPL) deficiency due to a nonsense mutation (Tyr302>Term) in exon 6 of LPL gene in an Italian family from Sardinia (LPL(Olbia)).

We analyzed the molecular defect in the lipoprotein lipase (LPL) gene of a young boy from Sardinia who had primary hyperchylomicronemia, pancreatitis, and a complete LPL deficiency in post-heparin plasma. Analysis of LPL gene was performed by using single strand conformation polymorphism (SSCP) and direct sequencing of SSCP-positive region. The proband was homozygous for a C > A transversion in exon 6, which converts the codon for tyrosine at position 302 into a termination codon and eliminates an RsaI restriction site; this allowed the rapid screening of the proband's family members, among whom nine heterozygotes and one additional homozygote were identified. The homozygote was the proband's paternal grandmother who had shown the first clinical manifestation (recurrent pancreatitis) of LPL deficiency at the age of 54 years. LPL mutation carriers showed a mild dyslipidemic phenotype characterized by a reduction of high density lipoprotein-cholesterol (HDL-C) levels, HDL-C/total cholesterol ratio, and low density lipoprotein (LDL) size, associated with a variable increase of triglyceride levels. Five of these carriers were also heterozygotes for beta-thalassemia (Q39X mutation). In these double mutation carriers, plasma HDL-C levels were higher and plasma triglycerides tended to be lower than in carriers of LPL mutation alone. The Tyr302 > Term mutation encodes a truncated protein of 301 amino acids that is probably not secreted by the LPL producing cells. This is the first mutation of LPL gene found in Sardinians.

Apolipoproteins E↗