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PubMed1993

p53 mutation is a common genetic event in ovarian carcinoma.

Using the single-strand conformational polymorphism technique, we have screened 66 malignant ovarian tumors for p53 mutation in exons 5 to 8. Thirty-four of the tumors demonstrated a single-strand conformational polymorphism band shift in this region of the gene, including 6 in exon 5, 7 in exon 6, 12 in exon 7, and 10 in exon 8 (one of the tumors showed a shift for exons 7 and 8). All of the single-strand conformational polymorphism shifts have been further characterized by DNA sequencing, and 31 of 35 have been shown to represent genuine DNA alterations. These include 27 point mutations (23 missense, 2 nonsense, and 2 silent mutations), 3 deletions (a 2-base pair deletion introducing, by frameshift, a stop codon further downstream; a 3-base pair deletion; and an unusual 6-base pair deletion made up of separate 2-base pair and 4-base pair deletions), and a 4-base pair insertion (introducing a stop codon downstream). In total, 29 of the 66 (44%) carcinomas analyzed had mutations affecting the primary sequence of the p53 protein. p53 mutation was found in tumors of all International Federation of Gynecologists and Obstetricians stages, suggesting that it might be an earlier genetic event in the progression of epithelial ovarian tumors than previously thought. A significantly greater number of p53 mutations were seen in high-grade serous carcinomas than in those of endometrioid and mucinous types (0.02 > P > 0.01). Analysis of the distribution of point mutations showed no preference for any particular mutation type.

Base Sequence↗
PubMed1997

Disruption of the varicella-zoster virus dUTPase and the adjacent ORF9A gene results in impaired growth and reduced syncytia formation in vitro.

Varicella-zoster virus (VZV) open reading frame 8 (ORF8) is predicted to encode the viral dUTPase and the adjacent gene, ORF9A, is thought to encode a membrane protein homologous to HSV-1 UL49.5. A fusion protein, in which the amino portion of glutathione-S-transferase was fused to amino acids 5 to 396 of VZV ORF8 protein, had dUTPase activity in vitro. Construction of a mutant VZV with stop codons or a deletion in the ORF8 gene resulted in loss of viral dUTPase activity. Antibody to VZV ORF9A protein demonstrated a 7-kDa protein located in the membranes of virus-infected cells. Insertion of stop codons into VZV ORF9A resulted in VZV that produced smaller plaques than parental virus. Inactivation of both VZV ORF8 and ORF9A resulted in a virus that grew to lower titers and was impaired for syncytia formation when compared to parental virus. In contrast, a similar mutation in HSV-1 has no effect on growth of the virus in vitro. These results identify loci in the VZV genome that are required for a syncytial phenotype in vitro.

Gene Deletion↗
PubMed1994

The evolution of proteins from random amino acid sequences: II. Evidence from the statistical distributions of the lengths of modern protein sequences.

This paper continues an examination of the hypothesis that modern proteins evolved from random heteropeptide sequences. In support of the hypothesis, White and Jacobs (1993, J Mol Evol 36:79-95) have shown that any sequence chosen randomly from a large collection of nonhomologous proteins has a 90% or better chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. The goal of the present study was to investigate the possibility that the random-origin hypothesis could explain the lengths of modern protein sequences without invoking specific mechanisms such as gene duplication or exon splicing. The sets of sequences examined were taken from the 1989 PIR database and consisted of 1,792 "super-family" proteins selected to have little sequence identity, 623 E. coli sequences, and 398 human sequences. The length distributions of the proteins could be described with high significance by either of two closely related probability density functions: The gamma distribution with parameter 2 or the distribution for the sum of two exponential random independent variables. A simple theory for the distributions was developed which assumes that (1) protoprotein sequences had exponentially distributed random independent lengths, (2) the length dependence of protein stability determined which of these protoproteins could fold into compact primitive proteins and thereby attain the potential for biochemical activity, (3) the useful protein sequences were preserved by the primitive genome, and (4) the resulting distribution of sequence lengths is reflected by modern proteins. The theory successfully predicts the two observed distributions which can be distinguished by the functional form of the dependence of protein stability on length. The theory leads to three interesting conclusions. First, it predicts that a tetra-nucleotide was the signal for primitive translation termination. This prediction is entirely consistent with the observations of Brown et al. (1990a,b, Nucleic Acids Res 18:2079-2086 and 18: 6339-6345) which show that tetra-nucleotides (stop codon plus following nucleotide) are the actual signals for termination of translation in both prokaryotes and eukaryotes. Second, the strong dependence of statistical length distributions on sequence-termination signaling codes implies that the evolution of stop codons and translation-termination processes was as important as gene splicing in early evolution. Third, because the theory is based upon a simple no-exon stochastic model, it provides a plausible alternative to a limited universe of exons from which all proteins evolved by gene duplication and exon splicing (Dorit et al. 1990, Science 250:1377-1382).

Amino Acid Sequence↗
PubMed1993

A single-copy relaxin-like gene sequence is present in sheep.

Relaxin is a peptide hormone which consists of two polypeptide chains that are synthesized as a B-chain/C-peptide/A-chain precursor. We have used the polymerase chain reaction (PCR) to isolate and clone a relaxin-like cDNA from sheep placental RNA. This cDNA and two sheep genomic clones were characterised by nucleotide sequencing. A comparison of the sheep nucleotide sequence with exon II of pig relaxin revealed homology of 72%. The sheep sequence had numerous stop codons in the region corresponding to the C-peptide. Therefore, there is no open reading frame which would include the C-peptide and A-chain regions. Analysis of several animals indicates that the stop codons are not due to an allelic polymorphism and Southern blot analysis of genomic DNA reveals the presence of a single copy gene. The 5' RACE PCR protocol was used to obtain sequence information for the 5' relaxin-like RNA. This analysis reveals that unprocessed precursor RNA is the predominant RNA species in placenta. A small proportion of clones was isolated which contained novel 5' sequences. These sequences mostly appear to be generated from repetitive DNA elements upstream of exon II. No relaxin-like exon I sequence which encodes the B-chain was found after an extensive search of the 5' RACE PCR products. Therefore, this relaxin-like gene does not produce an RNA species in ovary, placenta or endometrial tissue which could give rise to a functional sheep relaxin hormone.

Amino Acid Sequence↗
PubMed1995

Coding density of the turnip yellow mosaic virus genome: roles of the overlapping coat protein and p206-readthrough coding regions.

More than one-third of the turnip yellow mosaic virus (TYMV) genome simultaneously encodes two ORFs. We have investigated the functions of the overlapping coat protein ORF and readthrough domain of ORF-206 in the 3' region of the genome. TYMC-206 RNA, in which a second stop codon has been positioned to prevent ORF-206 readthrough, induced infections in protoplasts and plants that were indistinguishable from wild type. ORF-206 readthrough is thus nonessential. Nevertheless, TYMV-221 RNA, in which the ORF-206 stop codon was replaced with a tyrosine codon to force readthrough, was infectious to protoplasts, suggesting that a role for ORF-206 readthrough under certain conditions is possible. TYMV RNA variants that produce truncated or no coat protein were used to show that the coat protein is dispensable for local movement but necessary for systemic spread of virus in plants. Studies in protoplasts showed that (-) RNA levels are normal in the absence of coat protein, but (+) strand levels are decreased about 10-fold relative to wild-type infections. A mutant with a short C-terminal coat protein extension that formed virions less stable than normal demonstrated the protective role of capsids toward genomic RNA. The evolutionary implications of the dense information content of the TYMV genome are discussed.

Brassica↗
PubMed1999

Post-termination ribosome interactions with the 5'UTR modulate yeast mRNA stability.

A novel form of post-transcriptional control is described. The 5' untranslated region (5'UTR) of the Saccharomyces cerevisiae gene encoding the AP1-like transcription factor Yap2 contains two upstream open reading frames (uORF1 and uORF2). The YAP2-type of uORF functions as a cis-acting element that attenuates gene expression at the level of mRNA turnover via termination-dependent decay. Release of post-termination ribosomes from the YAP2 5'UTR causes accelerated decay which is largely independent of the termination modulator gene UPF1. Both of the YAP2 uORFs contribute to the destabilization effect. A G/C-rich stop codon context, which seems to promote ribosome release, allows an uORF to act as a transferable 5'UTR-destabilizing element. Moreover, termination-dependent destabilization is potentiated by stable secondary structure 3' of the uORF stop codon. The potentiation of uORF-mediated destabilization is eliminated if the secondary structure is located further downstream of the uORF, and is also influenced by a modulatory mechanism involving eIF2. Destabilization is therefore linked to the kinetics of acquisition of reinitiation-competence by post-termination ribosomes in the 5'UTR. Our data explain the destabilizing properties of YAP2-type uORFs and also support a more general model for the mode of action of other known uORFs, such as those in the GCN4 mRNA.

5' Untranslated Regions↗
PubMed1999

Resuming translation on tmRNA: a unique mode of determining a reading frame.

The bacterial ribosome switches from an mRNA lacking an in-frame stop codon and resumes translation on a specialized RNA known as tmRNA, SsrA or 10Sa RNA. We find that the ribosome can reach and use the extreme 3' terminal codon of the defective mRNA prior to switching. The first triplet to be translated in tmRNA (the resume codon) is determined at two levels: distant elements in tmRNA restrict resume codon choice to a narrow window and local upstream elements provide precision. Insights from a randomization-selection experiment secure the alignment of tmRNA sequences from diverse species. The triplet UA(A/G) (normally recognized as a stop codon by release factor-1) is strongly conserved two nucleotides upstream of the resume codon. The central adenosine of this triplet is essential for tmRNA activity. The reading frame of tmRNA is determined differently from all other known reading frames in that the first translated codon is not specified by a particular tRNA anticodon.

Amino Acid Sequence↗
PubMed1993

Epstein-Barr virus recombinants with specifically mutated BCRF1 genes.

Epstein-Barr virus (EBV) recombinants with specifically mutated BCRF1 genes were constructed and compared with wild-type BCRF1 recombinants derived in parallel for the ability to initiate and maintain latent infection and growth transformation in primary human B lymphocytes. A stop codon insertion after codon 116 of the 170-codon BCRF1 open reading frame or deletion of the entire gene had no effect on latent infection, B-lymphocyte proliferation into long-term lymphoblastoid cell lines (LCLs), or virus replication. LCLs infected with the stop codon recombinant were indistinguishable from wild-type recombinant-infected LCLs in tumorigenicity in SCID mice. However, mutant BCRF1 recombinant-infected cells differed from wild-type recombinant-infected cells in their inability to block gamma interferon release in cultures of permissively infected LCLs incubated with autologous human peripheral blood mononuclear cells. This is the first functional assay for BCRF1 expression from the EBV genome. BCRF1 probably plays a key role in modulating the specific and nonspecific host responses to EBV infection.

Animals↗
PubMed1999

Effect of cytoplasmic tail truncations on the activity of the M(2) ion channel of influenza A virus.

The M(2) protein of influenza A virus forms a proton channel that is required for viral replication. The M(2) ion channel is a homotetramer and has a 24-residue N-terminal extracellular domain, a 19-residue transmembrane domain, and a 54-residue cytoplasmic tail. We show here that the N-terminal methionine residue is cleaved from the mature protein. Translational stop codons were introduced into the M(2) cDNA at residues 46, 52, 62, 72, 77, 82, 87, and 92. The deletion mutants were designated truncx, according to the amino acid position that was changed to a stop codon. We studied the role of the cytoplasmic tail by measuring the ion channel activity (the current sensitive to the M(2)-specific inhibitor amantadine) of the cytoplasmic tail truncation mutants expressed in oocytes of Xenopus laevis. When their conductance was measured over time, mutants trunc72, trunc77, and trunc92 behaved comparably to wild-type M(2) protein (a decrease of only 4% over 30 min). In contrast, conductance decreased by 28% for trunc82, 27% for trunc62, and 81% for trunc52 channels. Complete closure of the channel could be observed in some cells for trunc62 and trunc52 within 30 min. These data suggest that a role of the cytoplasmic tail region of the M(2) ion channel is to stabilize the pore against premature closure while the ectodomain is exposed to low pH.

Amino Acid Sequence↗
PubMed1993

Tissue-specific microtubule functions in Drosophila spermatogenesis require the beta 2-tubulin isotype-specific carboxy terminus.

beta-Tubulins are encoded by members of multigene families and are generally highly conserved at the sequence level. The carboxyl terminal 15 amino acids are markedly more diverged than the rest of the sequence and constitute an "isotype defining region," which is conserved in corresponding beta-tubulin isoforms in different vertebrate species. It is thought that the carboxy terminus of beta-tubulin may not be required for assembly of microtubules per se, but it may be necessary for conferring properties on beta-tubulins required for isotype-specific functions. We have determined the extent to which a beta-tubulin isoform that lacks its carboxy terminus can assemble into functional suprastructures by generating two early-stop-codon variants of the gene for the testis-specific beta-tubulin (beta 2) in Drosophila melanogaster. We have also sequenced the null allele of this gene and discovered that it also contains an early-stop codon. By examining the products of these genes and the phenotypes they confer, we have determined that the beta-tubulin variants with large truncations (171 or 50 amino acids) do not accumulate to detectable levels and provide no beta-tubulin function. However, a small truncation missing only the terminal 15 amino acids is capable of being assembled into ultrastructurally normal looking microtubules in vivo, even though the truncated protein is less stable than wildtype beta 2. The functional failings of this truncated beta-tubulin are manifested in defective microtubule-based spermatogenic suprastructures, rather than at the level of assembly of individual microtubules. The most remarkable defect conferred by the truncated beta 2 is the failure of axonemes to assemble with proper organization, even though microtubules with presumptive axoneme identity are clearly present. We therefore demonstrate that the carboxy terminus of beta 2-tubulin is indeed required for organization of microtubule suprastructures in spermatogenesis. This observation supports the hypothesis that the variable carboxy terminus mediates isotype-specific microtubule-dependent functions.

Alleles↗
PubMed2004

Amino-terminal anchored surface display in insect cells and budded baculovirus using the amino-terminal end of neuraminidase.

Methods currently used for surface display on insect cells and budded baculovirus, all utilize the sequences from class I transmembrane proteins. This gives rise to some problems when handling unknown genes or cDNAs encoding full-length proteins. First, the stop codon from the cloned gene will be located upstream of the sequence for the transmembrane region. Second, the chance of getting the sequences encoding the signal peptide and the transmembrane region in frame with the cloned gene is small. To minimize these problems, we here present a method by which cDNAs or genes of interest can be cloned and fused to the codons for the signal peptide and transmembrane region of neuraminidase (NA), a class II transmembrane protein of the influenza virus. By placing both the signal peptide and transmembrane region at the amino-terminal, potential problems regarding stop codons are eliminated and errors in frame-shift minimized. To obtain proof of principle, the gene encoding enhanced green fluorescent protein, EGFP, was subcloned into a shuttle vector downstream of the neuraminidase sequence and the fusion product was then transferred to a baculovirus vector and transfected into insect cells (Sf9). Using this method, EGFP was found to be expressed on the surface of both infected cells and budded virus in an accessible manner.

Amino Acids↗
PubMed1998

Libraries of green fluorescent protein fusions generated by transposition in vitro.

Two artificial transposons have been constructed that carry a gene encoding Green Fluorescent Protein and can be used for generating libraries of GFP fusions in a gene of interest. One such element, AT2GFP, can be used to generate GFP insertions in frame with the amino acid sequence of the protein of interest, with a stop codon at the end of the GFP coding sequence; AT2GFP also contains a selectable marker that confers trimethoprim resistance in bacteria. The second element, GS, can be used to generate tribrid GFP fusions because there is no stop codon in the GFP transposon, and the resulting fusion proteins contain the entire amino acid sequence encoded by the gene. The GS element consists of a gfp open reading frame and a supF amber suppressor tRNA gene; the supF portion of the GS transposon can be utilized as a selectable marker in bacteria. Its sequence contains a fortuitous open reading frame, and thus it can be translated continuously with the gfp amino acid sequence. As a target for GFP insertions, we used a plasmid carrying the native Ty1 retrotransposon of the yeast Sacharomyces cerevisiae. The resulting multiple GFP fusions to Ty1 capsid protein Gag and Ty1 integrase were useful in determining the cellular localization of these proteins. Libraries of GFP fusions generated by transposition in vitro represent a novel and potentially powerful method to study the cell distribution and cellular localization signals of proteins.

Animals↗
PubMed2004

Genetic reprogramming by retroviruses: enhanced suppression of translational termination.

Viruses often exploit or subvert host machinery for their own purposes during replication. A search for proteins interacting with the murine leukemia virus reverse transcriptase (RT) recently provided a new example of such exploitation. RT was found to bind the eukaryotic translational release factor 1 (eRF1), the protein that recognizes stop codons and, in complex with eRF3, causes termination and polypeptide release from the ribosome. RT is derived from a large Gag-Pol polyprotein, and its synthesis requires a translational readthrough, a suppression of termination, at a stop codon at the end of the gag gene. The binding of eRF1 by RT was found to inhibit eRF1 action, enhance the efficiency of readthrough, and thus cause higher levels of RT synthesis. The observations suggest that retroviruses manipulate the translational machinery in sophisticated ways to fine-tune their own gene expression.

Codon, Terminator↗
PubMed1999

Novel mutations in Rsk-2, the gene for Coffin-Lowry syndrome (CLS).

Coffin-Lowry syndrome (CLS) is an X-linked disorder characterized by facial dysmorphism, digit abnormalities and severe psychomotor retardation. CLS had previously been mapped to Xp22.2. Recently, mutations in the ribosomal S6 kinase (Rsk-2) gene were shown to be associated with CLS. We have tested five unrelated individuals with CLS for mutations in nine exons of Rsk-2 using Single Strand Conformation Polymorphism (SSCP) analysis. Two patients had the same missense mutation (C340T), which causes an arginine to tryptophan change (R114W). This mutation falls just outside the N-terminal ATP-binding site in a highly conserved region of the protein and may lead to structural changes since tryptophan has an aromatic side chain whereas arginine is a 5 carbon basic amino acid. The third patient also had a missense mutation (G2186A) resulting in an arginine to glutamine change (R729Q). The fourth patient had a 2bp deletion (AG) of bases 451 and 452. This creates a frameshift that results in a stop codon 25 amino acids downstream, thereby producing a truncated protein. This deletion also falls within the highly conserved amino-catalytic domain of the protein. The fifth patient has a nonsense mutation (C2065T) which results in a premature stop codon, thereby producing a truncated protein. These mutations further confirm Rsk-2 as the gene involved in CLS and may help in understanding the structure and function of the protein.

Abnormalities, Multiple↗
PubMed1999

Immunochemical determination of cellular content of translation release factor RF4 in Escherichia coli.

The biosynthesis of proteins in prokaryotes is terminated when a stop codon is present in the A-site of the 70S ribosomal complex. Four different translation termination factors are known to participate in the termination process. Release factor RF1 and RF2 are responsible for the recognition of the stop codons, and RF3 is known to accelerate the overall termination process. Release factor RF4 is a protein involved in the release of the mRNA and tRNA from the ribosomal complex. Furthermore, RF4 is involved in the proofreading in the elongation step of protein biosynthesis. The cellular contents of RF1, RF2, and RF3 were determined earlier. Here we report the cellular content of RF4 in Escherichia coli to be approximately 16,500 molecules per cell. The cells were grown in a rich medium and harvested in the beginning of the exponential growth phase. The quantifications were performed by using Western immunoblotting with radioactive iodinated streptavidin and biotinylated rabbit anti-mouse immunoglobulins plus a highly specific monoclonal antibody against RF4 as first antibody.

Animals↗
PubMed2007

Carney complex: the first 20 years.

PURPOSE OF REVIEW: The purpose of this review is to comment on the current findings on Carney complex, a dominantly inherited disease and a unique multiple endocrine neoplasia syndrome. RECENT FINDINGS: Sequencing of the PRKAR1A gene in more than 150 kindreds has revealed a number of pathogenic mutations; in more than 90% of the cases, the sequence change was predicted to lead to a premature stop codon and, thus, mutant mRNAs were subject to nonsense-mediated mRNA decay. In Carney complex syndrome cells carrying these mutations, protein kinase A activity is irregularly stimulated by cAMP. Mutations that did not lead to a premature stop codon have also been described; these were also associated with abnormal protein kinase A activity. Animal models of the disease have been recently developed; they reproduced some of the stigmata of Carney complex syndrome but not all. Genetic testing of patients' family members has been introduced in recent years, leading to early detection and a better overall prognosis. SUMMARY: New treatments have yet to be applied; the elucidation of the molecular pathways regulated by PRKAR1A holds the promise of leading to molecularly designed therapies.

Acromegaly↗
PubMed1985

Translational coupling in Bacillus subtilis of a heterologous Bacillus subtilis-Escherichia coli gene fusion.

Translational coupling was demonstrated in a gene fusion in which the promoter and the N-terminal region of the Bacillus subtilis subtilisin (aprA) gene were fused to a promoterless Tn9-derived chloramphenicol acetyltransferase (CAT; EC 2.3.1.28) gene. Expression of this gene fusion results in the production of a native-sized CAT product, whereas the Tn9-derived CAT gene is usually not translated from its own ribosome binding site in B. subtilis (D. S. Goldfarb, R. L. Rodriguez, and R. H. Doi, Proc. Natl. Acad. Sci. USA 79:5886-5890, 1982). A 178-base-pair deletion, which removed part of the signal peptide and the propeptide of the aprA gene and created a translational stop codon 230 base pairs upstream of the CAT gene ribosome binding site, reduced expression of the CAT gene. A BamHI 10-mer linker insertion into this deletion site, which restored the reading frame and simultaneously removed the translation stop codon, restored CAT gene expression. The data indicate that expression of the CAT gene was dependent on translation of the truncated aprA gene into the ribosome binding site of the CAT gene.

Acetyltransferases↗
PubMed1985

Sequence structures of a mouse major urinary protein gene and pseudogene compared.

Laboratory mouse strains carry approximately 35 major urinary protein (MUP) genes per haploid genome, tightly clustered together on chromosome 4. Most belong to two main groups (Groups 1 and 2). The available evidence strongly suggests that the Group 1 genes are active while the Group 2 genes are pseudogenes. Here we present the complete sequence of a Group 1 gene and a Group 2 gene and 700 bp of flanking sequence. The sequence of the Group 1 gene is consistent with its being active. The Group 2 gene contains two stop codons and a frame-shift mutation in the reading frame defined by the Group 1 gene, and would code for a signal peptide 25 rather than 19 amino acids long. The Group 2 gene differs from the Group 1 gene in other ways: a deletion upstream of the TATA box and another in intron 3, a base change in the TATA box itself, a 2 bp duplication at the splice acceptor boundary of intron 6, an altered poly(A) addition signal and a 1-base deletion 5' to the initiation codon. Some of these differences may explain the 10- to 20-fold higher level of Group 1 mRNA in mouse liver, and the fact that Group 1 and Group 2 transcripts are mainly spliced differently. The presence of the stop codon means that the Group 2 gene is a pseudogene in the context of the Group 1 gene. However, there is some evidence that the mature hexapeptide that it would code for may have biological activity. The 12 acceptor splice sites of the two genes all contain the identical sequence ACAG at the exon boundary.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗