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PubMed1996

RNA-binding proteins of 37/38 kDa bind specifically to the barley chloroplast psbA 3'-end untranslated RNA.

The stability of the psbA mRNA increases during barley chloroplast development eventually reaching a half-life of over 40 h. Translation of psbA mRNA is also regulated in a complex way. Sequence-specific RNA binding proteins may modulate the translation or stability of the psbA mRNA during chloroplast development. UV cross-linking assays revealed that chloroplast proteins of 37 and 38 kDA bind specifically to the 3' end of psbA transcripts and not to the 5' end of psbA or rbcL transcripts. The two RNA-binding proteins were partially purified by ammonium sulfate precipitation followed by heparin agarose chromatography. Deletion and site-directed mutation analysis demonstrated that the 37/38RNPs bind in a 30 nucleotide region immediately downstream from the translation termination codon and upstream of sequences capable of forming a stem-loop structure in the 3' end of psbA transcripts. Single-base changes that diminish the binding of the 37RNP also reduce binding of the 38RNP suggesting that these proteins may bind as a heterodimer. The 37/38RNPs that bind within the 3' end of psbA transcripts could modulate transcription termination, translation or mRNA stability.

Base Sequence↗

PubMed2003

A possible approach to site-specific insertion of two different unnatural amino acids into proteins in mammalian cells via nonsense suppression.

The site-specific insertion of an unnatural amino acid into proteins in vivo via nonsense suppression has resulted in major advances in recent years. The ability to incorporate two different unnatural amino acids in vivo would greatly increase the scope and impact of unnatural amino acid mutagenesis. Here, we show the concomitant suppression of an amber and an ochre codon in a single mRNA in mammalian cells by importing a mixture of aminoacylated amber and ochre suppressor tRNAs. This result provides a possible approach to site-specific insertion of two different unnatural amino acids into any protein of interest in mammalian cells. To our knowledge, this result also represents the only demonstration of concomitant suppression of two different termination codons in a single gene in vivo.

Amino Acids↗

PubMed1997

Two mutated HEXA alleles in a Druze patient with late-infantile Tay-Sachs disease.

Two affected HEXA alleles were found in an Israeli Druze Tay-Sachs child born to first-cousin parents. His paternal allele contained two adjacent changes in exon 5: delta496C, which resulted in a frameshift and premature termination codon 96 nucleotides downstream, and 498C-->G, a silent mutation. The maternal allele had a 835T-->C transition in exon 8 (S279P). Phosphoimaging quantitation of the parents' RNAs showed that the steady-state levels of mRNAs of the mutant exons 5 and 8 were 5% and 50%, respectively, of normal levels. The exon 5 mutated allele with the premature translation termination resulted in severe deficiency of Hex A. Transient expression of the exon 8 mutated alpha-chain cDNA in COS-1 cells resulted in deficiency of enzymatic activity. The child exhibited a late-infantile-type disease.

Alleles↗

PubMed1996

Mutation analysis reveals an insertional hotspot in exon 4 of the LDL receptor gene.

Mutation analysis of the low density lipoprotein receptor (LDLR) gene revealed a novel 8-bp duplication after nucleotide 681 in a Costa Rican patient with familial hypercholesterolaemia. The frameshift caused by this mutation results in a premature termination codon in the EGF precursor homology domain of the mature LDLR, whereby a truncated protein of the first 206 residues with an additional 39 abnormal residues would be created. The insertion overlaps with previously described duplications of 18 bp and 21 bp, thus revealing an insertional hotspot in exon 4 of the LDLR gene. We propose that the structural features of this region of the LDLR gene contribute significantly to genetic instability and the subsequent DNA duplication via an endogenous sequence-directed mechanism of mutagenesis.

Amino Acid Sequence↗

PubMed1990

A single nucleotide deletion in codon 123 of the beta-globin gene causes an inclusion body beta-thalassaemia trait: a novel elongated globin chain beta Makabe.

The beta-globin gene from a Japanese individual with an inclusion body beta-thalassaemia trait has been characterized by gene cloning and DNA sequencing. An adenine deletion was detected at the first position of codon 123 (ACCCC) of one allele whereas the other allele had a normal sequence. Heterozygosity for this mutation in the patient was confirmed by Southern blots of the genomic DNA digested with HphI, the recognition site of which is eliminated by this deletion. This one base deletion results in the shift of a reading frame in such a manner that the normal termination codon is out of phase. This frameshift mutation results in the synthesis of an elongated beta-globin chain with 10 extra amino acid residues and with an altered C-terminus. Analysis of labelled globin chains using CM-cellulose column chromatography failed to demonstrate any abnormal protein, thereby suggesting that the beta-globin chain variant is highly unstable and probably degrades rapidly after synthesis. This event will lead to an accumulation of free alpha-chains precipitating in the red blood cells and an inclusion body beta-thalassaemia phenotype would ensue.

Amino Acid Sequence↗

PubMed1987

Mutational analysis of the 3' open reading frames and the splice junction at nucleotide 3225 of bovine papillomavirus type 1.

Functional analysis of the 3' open reading frames (ORFs) of bovine papillomavirus type 1 (BPV-1) has been complicated by the organization of that part of the genome. A region between nucleotides (nt) 3173 and 3551 contains three overlapping ORFs (E2, E3, and E4), as well as a 3' splice junction at nt 3225 which is used by many of the BPV-1 transcripts. To more clearly assign functions to specific ORFs in this region, single-base substitution mutations were generated which introduced translational termination codons into each of the three ORFs; a fourth mutation substituted an A with a C at nt 3223, altering the 3' splice junction consensus sequence from AG to CG. The E3- and the E4-specific mutants were wild type in their abilities to transform susceptible mouse C127 cells, to replicate as stable plasmids, and to trans-activate the E2 conditional enhancer. The E2-specific termination mutant was defective for plasmid replication, transformation, and trans-activation and could not be complemented for efficient transformation of a flat cell line which expressed the full-length E2 gene product. The splice junction mutant was defective for transformation of C127 cells and of a flat cell line expressing the full-length E2 gene product. These data extend previous analyses of the 3' ORFs and suggest that a spliced E2 product is involved in cellular transformation. The splice junction mutant could replicate as a stable plasmid, indicating that there is no absolute requirement in plasmid replication for a viral gene product expressed solely from an mRNA using the 3' splice junction at nt 3225.

Animals↗

PubMed1989

Cloning, expression and sequence analysis of the gene encoding the 120 kD surface-exposed protein of Rickettsia rickettsii.

Rickettsia rickettsii (R strain) genomic DNA was partially digested and cloned into the lambda expression vector gt11 generating a genomic clone bank. Transformant plaques were screened with antisera generated against the 120 kiloDalton protein of R. rickettsii to detect those phage expressing the recombinant protein. The gene encoding the 120 kD protein was localized to a 4.3 kilobase SphI-BamHI fragment from the recombinant phage and subcloned into pUC18 and pUC19. Full-length expression of the recombinant protein was achieved with both orientations. The gene and flanking regions were sequenced. The p120 gene consists of 3900 base pairs coding for 1300 amino acids. A distinguishable promoter region was not identified, although there are several 5' sequences that resemble classical prokaryotic promoters. Downstream of the termination codon for this gene lies a 726 base pair open reading frame on the opposite strand with the potential to encode a protein of approximately 27 kD. The identity of this putative gene product is unknown. The two open reading frames are separated by a 106 base pair intergenic region that consists of a stretch of dyad symmetry resembling rho-independent transcriptional terminators.

Amino Acid Sequence↗

PubMed2001

Glucocorticoid and mineralocorticoid resistance/hypersensitivity syndromes.

Glucocorticoids and mineralocorticoids regulate diverse functions important to maintain central nervous system, cardiovascular, metabolic, and immune homeostasis. The actions of these hormones are mediated by their specific intracellular receptors: the glucocorticoid (GR) and mineralocorticoid (MR) receptors. Pathologic conditions associated with changes of tissue sensitivity to these hormones have been described. The syndrome of familial glucocorticoid resistance is characterized by hypercortisolism without Cushing's syndrome stigmata. The molecular defects of four kindreds and one sporadic case have been elucidated as inactivating mutations in the ligand-binding domain of GR. Two cases developed glucocorticoid resistance at the heterozygous state. In these patients, mutant receptors possessed transdominant negative activity upon the wild type receptor. Insensitivity to mineralocorticoids (which may also be caused by loss of function mutations of the MR gene) was found in one sporadic case and four autosomal dominant cases of Pseudohypoaldosteronism type 1. These included two frameshift mutations and a premature termination codon in exon 2, leading to gene products lacking the entire DNA- and ligand-binding domains, and a single base-pair deletion in the intron-5 splice donor site. Tissue hypersensitivity to glucocorticoids was recently hypothesized in patients with Human Immunodeficiency Virus (HIV) type-1 infection via the accessory proteins Vpr and Tat which enhance GR transactivation. Since HIV-1 long terminal repeat (LTR) and glucocorticoid-responsive promoters use the same set of coactivators, these proteins may stimulate HIV-1-LTR and glucocorticoid-inducible genes concurrently. The former may directly stimulate viral proliferation, while the latter may indirectly enhance viral propagation by suppressing the host immune system through glucocorticoid-mediated mechanisms.

Acquired Immunodeficiency Syndrome↗

PubMed1987

The cDNA-deduced primary structure of human sex hormone-binding globulin and location of its steroid-binding domain.

We have sequenced a cDNA for sex hormone-binding globulin (SHBG) isolated from a phage lambda gt11 human liver cDNA library. The library was screened with a radiolabeled rat androgen-binding protein (ABP) cDNA, and the abundance of SHBG cDNAs was 1 in 750,000 plaques examined. The largest human SHBG cDNA (1194 base-pairs) contained a reading frame for 381 amino acids. This comprised 8 amino acids of a signal peptide followed by 373 residues starting with the known NH2-terminal sequence of human SHBG, and ending with a termination codon. The predicted polypeptide Mr of SHBG is 40,509, and sites of attachment of one O-linked (residue 7) and two N-linked oligosaccharide (residues 351 and 367) chains were identified. Purified SHBG was photoaffinity-labeled with delta 6-[3H]testosterone and cleaved with trypsin. The labeled tryptic fragment was isolated by reverse-phase HPLC, and its NH2-terminal sequence was determined. The results suggest that a portion of the steroid-binding domain of SHBG is located between residue 296 and the 35 predominantly hydrophilic residues at the C-terminus of the protein.

Amino Acid Sequence↗

PubMed1992

Primary structure of an archaebacterial transducer, a methyl-accepting protein associated with sensory rhodopsin I.

A methylated membrane protein of 97 kDa was suggested on the basis of mutant analysis to transduce signals from the phototaxis receptor sensory rhodopsin I to the flagellar motor in Halobacterium halobium. Here we report isolation of the proposed transducer protein, cloning of its gene based on partial protein sequences, the complete gene sequence, and analysis of the encoded primary structure. The 1611-base-pair gene termination codon overlaps the initiator ATG of the sopI gene, which encodes the sensory rhodopsin I apoprotein. The predicted size of 57 kDa for the methylated protein indicates an aberrant electrophoretic migration on SDS/polyacrylamide gels, as occurs with other acidic halophilic proteins. Putative promotor elements are located in an A+T-rich region upstream of the gene. Comparison of the translated nucleotide sequence with N-terminal sequence of the purified protein shows the protein is synthesized without a processed leader peptide and the N-terminal methionine is removed in the mature protein. The deduced protein sequence predicts two transmembrane helices near the N terminal that would anchor the protein to the membrane. Beyond this hydrophobic region of 46 residues, the remainder of the protein (536-amino acid residues total) is hydrophilic. The C-terminal 270 residues contain a region homologous to the signaling domains of eubacterial transducers (e.g., Escherichia coli Tsr protein), flanked by two regions homologous to the methylation domains of the transducer family. The protein differs from E. coli Tsr in that it does not have an extramembranous-receptor binding domain but instead has a more extended cytoplasmic region. Coexpression of the methyl-accepting protein gene (designated htrI) and sopI restores sensory rhodopsin I phototaxis to a mutant (Pho81) that contains a deletion in the htrI/sopI region. These results extend the eubacterial transducer family to the archaebacteria and substantiate the proposal that the methylated membrane protein functions as a signal-transducing relay between sensory rhodopsin I and cytoplasmic sensory-pathway components.

Amino Acid Sequence↗

PubMed1990

An antifreeze glycopeptide gene from the antarctic cod Notothenia coriiceps neglecta encodes a polyprotein of high peptide copy number.

The antarctic fish Notothenia coriiceps neglecta synthesizes eight antifreeze glycopeptides (AFGP 1-8; Mr 2600-34,000) to avoid freezing in its ice-laden freezing habitat. We report here the sequence of one of its AFGP genes. The structural gene contains 46 tandemly repeated segments, each encoding one AFGP peptide plus a 3-amino acid spacer. Most of the repeats (44/46) code for peptides of AFGP 8; the remaining 2 code for peptides of AFGP 7. At least 2 of the 3 amino acids in the spacers could act as substrate for chymotrypsin-like proteases. The nucleotide sequence between the translation initiation codon (ATG) and the first AFGP-coding segment is G + T-rich and encodes a presumptive 37-residue signal peptide of unusual sequence. Primer extension establishes the transcription start site at nucleotide 43 upstream from ATG. CAAT and TATA boxes begin at nucleotides 53 and 49, respectively, upstream from the transcription start site. The polyadenylylation signal, AATAAA, is located approximately 240 nucleotides downstream from the termination codon. A mRNA (approximately 3 kilobases) was found that matches the size of this AFGP gene. Thus, this AFGP gene encodes a secreted, high-copy-number polyprotein that is processed posttranslationally to produce active AFGPs.

Amino Acid Sequence↗

PubMed1974

Mutants of yeast defective in iso-1-cytochrome c.

A medium containing chlorolactate has been devised to enrich for mutants that are unable to utilize lactate for growth, and therefore that may be defective in cytochrome c. Complementation tests of 6,520 chlorolactate-resistant mutants that were obtained spontaneously or induced with UV, ICR-170, or nitrosoimidazolidone resulted in the identification of 195 mutations at the cyc1 locus, which controls the primary structure of iso-1-cytochrome c. These 195 mutants, with 16 cyc1 mutants previously isolated, were examined for total cytochrome c by spectroscopic methods, growth on lactate medium, suppressibility by defined nonsense suppressors, mutational sites by x-ray-induced recombination, ability to revert, and in 86 cases, whether intragenic revertants contain altered iso-1-cytochrome c. Except for the deletion mutant cyc1-1, all of the mutants appeared to contain single-site mutations that could be assigned to at least 35 different sites within the gene. The cyc1 mutants either completely lacked iso-1-cytochrome c or contained iso-1- cytochromes c that were completely or partially nonfunctional. In spite of the fact that the cyc1 mutants obtained by the chlorolactate procedure were selected on the basis of defective function, 68% appeared to completely lack iso-1-cytochrome c. The remaining cyc1 mutants contained below normal amounts of iso-1-cytochromes c. Studies at several incubation temperatures indicated that these nonfunctional iso-1-cytochromes c were thermolabile. It is suggested that the predominant means for abolishing iso-1-cytochrome c by mutations are either through a complete loss, such as produced by chain terminating codons, or impairments through drastic changes of tertiary structure which lead to instability and thermolability.

Acridines↗

PubMed2001

The R71G BRCA1 is a founder Spanish mutation and leads to aberrant splicing of the transcript.

In a BRCA1 screening in familial breast cancer carried out in different centres in Spain, France, and United Kingdom, a missense mutation 330A>G which results in a Arg to Gly change at codon 71 (R71G) was independently identified in 6 families, all of them with Spanish ancestors. This residue coincides with the -2 position of the exon 5 donor splice site. We further investigated the effect of this base substitution on the splicing of BRCA1 mRNA. The sequence analysis of the cDNA indicated that 22 bp of exon 5 were deleted, creating with the first bases of exon 6 a termination codon at position 64, which results in a truncated protein. The BRCA1 haplotype of the R71G carrier patients and Spanish controls was analysed by use of six microsatellites located within or near BRCA1. Our results are consistent with the possibility that these families shared a common ancestry with BRCA1 R71G being a founder mutation of Spanish origin.

Age of Onset↗

PubMed1998

Different ocular abnormalities in individuals of a three-generation family caused by a new nonsense mutation in the PST domain of the PAX6 gene. Mutations in brief no. 189. Online.

PAX6 is a candidate gene for familial aniridia. We have carried out a mutational analysis of the PAX6 gene in a three-generation family from Germany, containing 5 individuals affected with ocular abnormalities. In all affected individuals, a heterozygous mutation was detected in the PAX6 gene, exchanging tyrosine 369 by a stop codon. The mutation is located in the 3' moiety of the PST domain, at the C terminus of the PAX6 protein. In the affected family members, the same heterozygous mutation leads to distinct phenotypes of varying severity. Most notably, no aniridia was observed in one of the family members carrying the mutation, although other ocular abnormalities (underdeveloped iris and cataracts) were present. We discuss the possibility that small C terminal truncations of the PAX6 protein might lead to less severe or more divergent phenotypes than trancations at internal positions.

Aniridia↗

PubMed1984

The nucleotide sequence at the recombination/integration sites of the hybrid viruses Ad2+ND3 and Ad2+ND5.

The nucleotide sequence at the recombination/integration sites of the adenovirus 2-simian virus 40 hybrid viruses, Ad2+ND3 and Ad2+ND5, is reported. These viruses were obtained by passages through human cells and fail to express the SV40-related proteins. The lack of expression of SV40-related proteins has been explained on the basis of the nucleotide sequence at the recombination sites. Ad2+ND3 has the entire reading frame for the SV40 T antigen removed up to the translation termination codon. The recombination event in Ad2+ND5 was found to occur in the leader region 11 nucleotides upstream from the splice junction, thus totally eliminating the naturally occurring splice site, which might have lead to defective processing of the mRNA. Alternatively, because of the large deletion, this virus is incapable of making similar hybrid proteins as in Ad2+ND1, Ad2+ND2, and Ad2+ND4, which share the N-terminal sequence of the 16-kDa glycoprotein of the wild-type virus. Thus, either one or both of these events may explain the lack of synthesis of the SV40 T antigen specific protein. Ad2+ND3 and Ad2+ND5 share the sequences at the right junction which suggests their origin from a common precursor. Also, the recombination was found to result in the disruption of the poly (A) addition signal of the adenovirus 2 early region III transcripts. All of the junction sequences were found to be rich in A:T base pairs.

Adenoviruses, Human↗

PubMed1990

TGATG vector: a new expression system for cloned foreign genes in Escherichia coli cells.

A TGATG vector system was developed that allows for the construction of hybrid operons with partially overlapping genes, employing the effects of translational coupling to optimize expression of cloned cistrons in Escherichia coli. In this vector system (plasmid pPR-TGATG-1), the coding region of a foreign gene is attached to the ATG codon situated on the vector, to form the hybrid operon transcribed from the phage lambda PR promoter. The cloned gene is the distal cistron of this hybrid operon ('overlappon'). The efficiently translated cro'-cat'-'trpE hybrid cistron is proximal to the promoter. The coding region of this artificial fused cistron [the length of the corresponding open reading frame is about 120 amino acids (aa)] includes the following: the N-terminal portions of phage lambda Cro protein (20 aa), the CAT protein of E. coli (72 aa) and 3' C-terminal codons of the E. coli trpE gene product. At the 3'-end of the cro'-cat'-'trpE fused cistron there is a region for efficient translation reinitiation: a Shine-Dalgarno sequence of the E. coli trpD gene and the overlapping stop and start codons (TGATG). In this sequence, the last G is the first nucleotide of the unique SacI-recognition site (GAGCT decreases C) and so integration of the structural part of the foreign gene into the vector plasmid may be performed using blunt-end DNA linking after the treatment of pPR-TGATG-1 with SacI and E. coli DNA polymerase I or its Klenow fragment.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1984

The sequence of a cloned cDNA for the beta subunit of bovine thyrotropin predicts a protein containing both NH2-and COOH-terminal extensions.

Cloned cDNAs containing sequences coding for the beta subunit of bovine thyrotropin have been identified. The complete nucleotide sequence of the largest of the beta subunit cDNA inserts has been determined. This cDNA contains 35 nucleotides from the 5' untranslated region of thyrotropin beta subunit mRNA and 60 nucleotides coding for an NH2-terminal precursor segment. This is followed by 339 nucleotides which code for the published amino acid sequence of the thyrotropin beta subunit. Following the 339 nucleotide beta subunit coding sequence, no termination codon is encountered for another 15 nucleotides. Thus, the cDNA codes for a thyrotropin beta subunit containing an additional 5 amino acids at the COOH terminus. The cDNA also contains 82 nucleotides of 3' untranslated sequence followed by a short poly(A) segment. Comparison of the bovine cDNA sequence to the recently described mouse thyrotropin beta subunit cDNA sequence reveals considerable homology throughout the coding sequence, including the COOH-terminal extension. These findings suggest the possibility that a thyrotropin beta subunit precursor is processed at both the NH2 and COOH termini.

Amino Acid Sequence↗

PubMed1997

The carboxy-terminal two-thirds of the cowpea chlorotic mottle bromovirus capsid protein is incapable of virion formation yet supports systemic movement.

Previous investigations into recombination in cowpea chlorotic mottle bromovirus (CCMV) resulted in the recovery of an unusual recombinant virus, 3-57, which caused a symptomless infection of cowpeas but formed no detectable virions. Sequence analysis of cDNA clones derived from 3-57 determined that mutations near the 5' terminus of the capsid protein gene introduced an early translational termination codon. Further mutations introduced a new in-frame start codon that allowed translation of the 3' two-thirds of the capsid protein gene. Based on the mutations observed in 3-57, wild-type CCMV clones were modified to determine if the carboxyl two-thirds of the capsid protein functions independently of the complete protein in long-distance movement. Analysis of these mutants determined that while virion formation is not required for systemic infection, the carboxy-terminal two-thirds of the capsid protein is both required and sufficient for systemic movement of viral RNA. This indicates that the CCMV capsid protein is multifunctional, with a distinct long-distance movement function in addition to its role in virion formation.

Bromovirus↗