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PubMed2001

Identification of endogenous SsrA-tagged proteins reveals tagging at positions corresponding to stop codons.

The SsrA.SmpB quality control system adds a C-terminal degradation peptide (AANDENYALAA) to nascent chains on stalled ribosomes, thereby freeing the ribosome and ensuring proteolysis of the tagged protein. An SsrA mutant with the tag sequence AANDEHHHHHH was used to slow degradation and facilitate Ni2+-nitrilotriacetic acid affinity purification. Display of affinity-purified Escherichia coli proteins on two-dimensional gels revealed small quantities of a diverse set of SsrA-H6-tagged proteins, and mass spectroscopy identified LacI repressor, lambda cI repressor, YbeL, GalE, RbsK, and a SlyD-kan(R) fusion protein as members of this set. For lambda repressor and YbeL, the SsrA-H6 tag was added after the natural C terminus of the protein, suggesting that tagging occurred while the ribosome idled at the termination codon of these genes. Potential causes of tagging for the other proteins include interference from translation of downstream reading frames, rare codons, and gene disruption. These and previous results support a broad role for the SsrA.SmpB system in freeing stalled ribosomes and in directing degradation of the products of these frustrated protein synthesis reactions.

Amino Acid Sequence↗

PubMed2002

A novel strategy by the action of ricin that connects phenotype and genotype without loss of the diversity of libraries.

We present a novel strategy for connection of phenotype and genotype in vitro that can be used for the selection of functional proteins even at room temperature. The strategy involves generation of a stable complex between a ribosome, an mRNA, and its translated protein, without removal of the termination codon, as a result of the action of the ricin A chain during translation. We demonstrate the potential selection capacity of this novel strategy by isolating such complexes that contain newly synthesized streptavidin and glutathione-S-transferase (GST) using appropriate ligands. The technique requires no transfection, no chemical synthesis, no ligation, and no removal of the termination codon. Thus our novel "Ribosome-Inactivation Display System (RIDS)" should provide, without loss of the pool population, a reliable, simple, and robust selection system for in vitro evolution of the properties of proteins in a predictable direction by a combination of randomization and appropriate selection strategies.

Gene Expression Profiling↗

PubMed1983

Chemical synthesis and molecular cloning of a STOP oligonucleotide encoding an UGA translation terminator in all three reading frames.

We have chemically synthesized an oligonucleotide 5'd(TGATTGATTGA)3' 3'd(ACTAACTAACT)5' that encodes the translation termination codon TGA in all three reading frames. After ligation of appropriate restriction endonuclease linkers to the ends, the double-stranded oligonucleotide (STOP-oligonucleotide) was joined to the plasmid pBR322 between the EcoRI and BamHI, or HindIII and BamHI sites, and the hybrid plasmids were transformed into Escherichia coli HB101. Four different constructions were obtained: (i) EcoRI-STOP-BamHI (STOP-oligonucleotide flanked by EcoRI and BamHI linkers; pKTH606), (ii) HindIII-STOP-BamHI (pKTH601), (iii) BamHI-STOP-HindIII (pKTH604), and (iv) HindIII-STOP-POTS-BamHI (two STOP-oligonucleotides in opposite orientation; pKTH605). The inserts in pKTH606 and pKTH601 were excised and transferred to a modified plasmid constructed previously for the expression and secretion of foreign gene products from Bacillus subtilis. The resulting secretion plasmids now contain the promoter/signal sequence region of the alpha-amylase gene from Bacillus amyloliquefaciens joined to the STOP-oligonucleotide by EcoRI or HindIII linkers. Foreign genes can be cloned into these sites. The plasmids can be used to express foreign genes truncated at their C-terminal end and therefore lacking their own translation termination codon. One such plasmid has been successfully used to express the Semliki Forest virus (SFV) membrane protein E1 truncated at its C-terminus.

Bacillus subtilis↗

PubMed1999

Antigen structure and genetic basis of histo-blood groups A, B and O: their changes associated with human cancer.

Three areas of research involved in blood group (or histo-blood group) ABO antigens and their genes, developed by our research group, are reviewed: (1) Antigen structures. The structural basis of A and H, A(1) and A(2), i and I antigens expressed in erythrocyte membranes. Major carriers of A and H determinants in erythrocytes are type 2 chain poly-LacNAc, short vs. long and unbranched vs. branched structures termed A(a), A(b), A(c), A(d) and H(1), H(2), H(3), H(4). Regular A (A(1)) and weak A (A(2)) were identified respectively as repetitive A (type 3 chain A) and A-associated H. A(1)- and A(2)-specific type 3 chain A and H, type 1 chain (representing Lewis blood group antigens), and type 4 chain (globo-series antigen; an extremely minor component in erythrocytes) are all glycosphingolipids. A and H determinants in fetal and newborn erythrocytes are carried by unbranched poly-LacNAc, whereas these determinants in adult erythrocytes are carried by branched poly-LacNAc. (2) ABO genes. A few cDNAs encoding A enzyme (UDP-GalNAc: H-a-GalNAc transferase) were cloned based on the amino acid sequence of purified A enzyme and their structures were compared with those of homologous cDNA from blood cells of B and O individuals (genotype BB, OO). Four nucleotide substitutions and four corresponding amino acid sequences essential for expression of A(1) allele and B allele, and differences between A and B enzymes, were identified. Amino acids 266 and 268, i.e. Leu and Gly for A enzyme vs. Met and Ala for B enzyme, were dominant in determining A vs. B activity (presumably recognizing UDP-GalNAc vs. UDP-Gal). The A(2) allele was characterized by deletion of the termination codon, extending nucleotides up to 1128 and thus encoding 21 extra amino acids at the C terminus, which may affect (diminish) the dominant function of amino acids 266 and 268. Typical O allele (O(1)) is characterized by deletion of nucleotide 261 G, causing frame shift and encoding of an entirely different, short polypeptide, due to appearance of early termination codon at nucleotide 354. Structures of other O alleles (O(1 v), O(2)) and other weak A alleles (A(3), A(el)) are also described. The genomic structure of ABO genes consists of seven exons which span approximately 19 kb of genomic DNA on chromosome 9, band q34. Most of the coding sequence is located in exon 7. Analysis of the 5' upstream region revealed the presence of the binding site for transcription factors and enhancer element. (3) Antigens and genes in cancer. A and B phenotypes aberrantly expressed in various types of human cancer, and their genetic basis, have been studied. One widely-occurring change observed in a large variety of human cancers is deletion of A or B epitope, associated with accumulation of their precursor H (Le(y), Le(b)), which causes enhanced malignancy. A less-commonly observed change is expression of incompatible A, identified as real type 1 chain A, in tumors of O or B individuals. A possible molecular genetic mechanism leading to such phenotypic changes is discussed.

ABO Blood-Group System↗

PubMed2004

[Further study on heterogeneic basis of complement C8 beta deficiency].

OBJECTIVE: In Caucasian population, the most common molecular basis for C8 beta deficiency s a single C to T transition in exon 9 of C8 beta gene resulting in a stop codon. In previous family studies, two individuals were identified with C8 beta complete deficiency and were found to be only heterozygous for this mutation. This study was conducted by the present authors in search of other possible causes for these two C8 beta deficient individuals. METHODS: Using direct DNA sequence analysis of all exon-specific PCR products of the C8 beta gene from these two C8 beta deficient patients and their descendants. RESULTS: Two other C to T transitions at base 298 and 388 in exon 3 were detected, which could also create a termination codon. The descendants from one of the deficient patients were also analysed for the mutations, and it could be demonstrated that the two C to T mutations in exons 9 and 3 are segregating independently. CONCLUSION: These two mutations, which create a termination codon, are sufficient to explain the complete C8 beta deficiency in both patients.

Codon, Nonsense↗

PubMed2003

A block in virus-like particle maturation following assembly of murine leukaemia virus in insect cells.

Expression of the murine leukaemia virus (MLV) major Gag antigen p65(Gag) using the baculovirus expression system leads to efficient assembly and release of virus-like particles (VLP) representative of immature MLV. Expression of p180(Gag-Pol), facilitated normally in mammalian cells by readthrough of the p65(Gag) termination codon, also occurs efficiently in insect cells to provide a source of the MLV protease and a pattern of p65(Gag) processing similar to that observed in mammalian cells. VLP release from p180(Gag-Pol)-expressing cells however remains essentially immature with disproportionate levels of the uncleaved p65(Gag) precursor when compared to the intracellular Gag profile. Changing the p65(Gag) termination codon altered the level of p65(Gag) and p180(Gag-Pol) within expressing cells but did not alter the pattern of released VLP, which remained immature. Coexpression of p65(Gag) with a fixed readthrough p180(Gag-Pol) also led to only immature VLP release despite high intracellular protease levels. Our data suggest a mechanism that preferentially selects uncleaved p65(Gag) for the assembly of MLV in this heterologous expression system and implies that, in addition to their relative levels, active sorting of the correct p65(Gag) and p180(Gag-Pol) ratios may occur in producer cells.

Animals↗

PubMed1993

Molecular characterization of Hb H disease by polymerase chain reaction.

We utilized the PCR method to amplify the alpha-thalassemia-1 breakpoint area of the Southeast Asia type and several regions of the alpha-globin gene cluster to diagnose rightward deletion (-alpha 3.7), leftward deletion (-alpha 4.2) or nondeletion forms of the Hb H disease. For the nondeletion form, a natural restriction site of MseI was used to detect the Hb Constant Spring (Hb CS) or other termination codon mutations. Another naturally occurring restriction site of MspI was used to detect the Hb Quong-Sze. For the deletion form of the Hb H disease, the differences among nonhomologous I, II and III of the rightward or leftward deletion were used to distinguish the mutations. For further characterization of the subtype of -alpha 3.7 deletion, the same primers for detecting termination codon mutations were used to amplify part of the alpha-globin gene, then the PCR product was digested by the restriction enzyme ApaI. In the 57 cases which were studied, 19 were deletion forms while 38 were nondeletion forms. In the deletion form cases, 13 were rightward deletion (-alpha 3.7) and the other 6 were leftward deletion (-alpha 4.2). However, all of the nondeletion form cases were alpha-thalassemia-1 with Hb CS. After the subtyping of -alpha 3.7 deletion, 11 out of 13 were type I deletions and the other 2 were type II deletions.

Adolescent↗

PubMedDate not supplied

A synthetic translation-terminator gene. A tool for dissecting the translation direction of a gene.

A 41-nucleotide-long duplex DNA, which contains the translation termination codon TAA in six reading frames and lactose operator sequence of Escherichia coli, has been synthesized. This fragment may be useful not only for producing a truncated protein encoded in a plasmid, but also for the identification of the precise coding region and translation direction of a bacterial gene in the cloned chromosomal segment. The synthetic fragment was inserted into beta-lactamase structural gene in pBR322 in order to test the in vivo activity. The plasmid produced mutant beta-lactamase reduced in size, as expected from the insertion site, and rendered the host bacterium constitutive for beta-galactosidase. Thus, termination codons and lactose operator in synthetic nucleotide appear to be functional in vivo.

Base Sequence↗

PubMed1999

Identification and characterization of mutations in patients with holocarboxylase synthetase deficiency.

Holocarboxylase synthetase deficiency (HCS) is an autosomal recessive disorder characterized by metabolic ketoacidosis, abnormal urine organic metabolites, and dermatitis. These symptoms are improved by pharmacological doses of biotin. In this study, we have analyzed seven patients with HCS deficiency found in European and Middle Eastern countries by using reverse transcription/polymerase chain reaction/single-stranded conformation polymorphism and a sequencing analysis. Although we had previously reported that two mutations were frequent in Japanese patients, no frequent mutations were found in the patients analyzed in this study. Seven novel mutations were identified in the cDNA of the patients; these included three missense mutations, two single-base deletions that resulted in a termination codon, a three-base in-frame deletion, and a 68-bp deletion. A new polymorphism C1121T was also identified in four alleles. A transient expression study demonstrated that the HCS activities of three missense mutations and one amino acid deletion were 1%-14% that of wild-type cDNA; in contrast, the activities of the two single-base deletions followed by a termination codon and Asp571Asn were nearly undetectable. These data suggest that a variety of mutations is responsible for decreasing HCS activity and that the aspartate residue at amino acid position 571 may be crucial for the catalytic activity of HCS.

Carbon-Nitrogen Ligases↗

PubMed1992

In vitro mutagenesis of biologically active transcripts of beet necrotic yellow vein virus RNA 2: evidence that a domain of the 75-kDa readthrough protein is important for efficient virus assembly.

RNA 2 of the multipartite genome of beet necrotic yellow vein virus carries the cistron for 21-kDa viral coat protein at its 5' extremity. The amber termination codon of the coat protein cistron undergoes suppression approximately 10% of the time so that translation continues into an adjacent 54-kDa open reading frame, yielding a 75-kDa readthrough protein. The roles of coat protein and the readthrough protein in infection were investigated with biologically active transcripts of RNA 2. Much of the coat protein cistron of the RNA 2 transcript could be deleted without interfering with viral replication and local lesion formation on leaves, although formation of the rod-shaped virions did not occur. Mutants in which the amber coat protein termination codon was replaced with an ochre codon or a tyrosine codon were also viable. The ochre codon was suppressed both in vitro and in planta. The mutant containing the tyrosine substitution produced only the 75-kDa read-through protein and was deficient in viral assembly. Deletions in the 54-kDa readthrough domain were also viable in planta but had different effects on virus assembly. A deletion in the C-terminal portion of the readthrough domain did not interfere with RNA packaging but, unexpectedly, deletions in the N-terminal portion were assembly deficient, although 21-kDa coat protein was produced in planta. Thus, the 75-kDa protein can apparently intervene in virion assembly even though it has not been detected in purified virions.

Base Sequence↗

PubMed2006

Nascent chain, mRNA, and ribosome complexes generated by a pure translation system.

Ribosome display is based on the concept that ternary complexes consisting of a nascent chain, ribosome, and mRNA can be generated, thereby establishing the linkage between genotype and phenotype that is essential for evolutionary experiments. With cell extract-based in vitro translation systems, it has been shown that ternary complexes can be generated by omitting the termination codon from the constructs, which can be stabilized at low temperature in the presence of high Mg2+ concentrations. Using an Escherichia coli-based reconstituted in vitro translation system (PURE system), in which all components necessary for the translation reaction were highly purified and reconstituted, ternary complexes could be generated equally well with a variety of sequences at the 3' end of the RNA, even those with a termination codon. Moreover, the generated complexes were stable at temperatures between 4 and 50 degrees C, and are thus highly stable in contrast to previous assumptions.

Cell-Free System↗

PubMed1998

Novel ITGB4 mutations in lethal and nonlethal variants of epidermolysis bullosa with pyloric atresia: missense versus nonsense.

Epidermolysis bullosa with pyloric atresia (EB-PA), an autosomal recessive genodermatosis, manifests with neonatal cutaneous blistering associated with congenital pyloric atresia. The disease is frequently lethal, but nonlethal cases have also been reported. Expression of the alpha6 beta4 integrin is altered at the dermal-epidermal basement-membrane zone; recently, mutations in the corresponding genes (ITGA6 and ITGB4) have been disclosed in a limited number of patients, premature termination codons in both alleles being characteristic of lethal variants. In this study, we have examined the molecular basis of EB-PA in five families, two of them with lethal and three of them with nonlethal variants of the disease. Mutation analysis disclosed novel lesions in both ITGB4 alleles of each proband. One of the patients with lethal EB-PA was a compound heterozygote for premature termination-codon mutations (C738X/4791delCA), whereas the other patient with a lethal variant was homozygous for a missense mutation involving a cysteine residue (C61Y). The three nonlethal cases had missense mutations in both alleles (C562R/C562R, R1281W/R252C, and R1281W/R1281W). Immunofluorescence staining of skin in two of the nonlethal patients and in one of the lethal cases was positive, yet attenuated, for alpha6 and beta4 integrins. These results confirm that ITGB4 mutations underlie EB-PA and show that missense mutations may lead to nonlethal phenotypes.

Antigens, CD↗

PubMed1996

The relative levels of alpha 2-, alpha 1-, and zeta-mRNA in HB H patients with different deletional and nondeletional alpha-thalassemia determinants.

We have analyzed the alpha 2/alpha 1-, alpha/beta-, zeta/(alpha + zeta)-mRNA ratios in the retic-ulocytes of 40 patients with Hb H disease. 21 patients had deletional Hb H disease (- -/- alpha), namely combinations of one of four types of alpha-thal-1 (MED-I, MED-II, -(alpha)20.5, SEA) and one of two types of alpha-thal-2 (-3.7 or -4.2 kb); 13 had Hb H disease because of combinations of one of these alpha-thal-1 deletions with either a 5 nt deletion at the 5' splicing site of IVS-I, or a terminating codon mutation (Hb CS), or a poly(A) mutation, and six were homozygous for either a poly(A) mutation or the 5 nt deletion. Significant differences were observed between the deletional types (- -/- alpha; alpha 2/alpha 1 ratio of zero; alpha/beta ratio of approximately 1) and non-deletional types (- -/alpha T alpha; alpha 2/alpha 1 ratio of 0.05-0.3 for those with T = the 5 nt deletion or the terminating codon mutant, and approximately 1.0 for those with T = a poly(A) mutation; alpha/beta ratio in all types of approximately 0.7). Comparable data were found for the nondeletional alpha-thal-2 homozygotes. The noted differences were highly significant and the determination of the two ratios may be diagnostically of considerable value. The low alpha 2/alpha 1-mRNA ratio in the two patients with - -/alpha-5nt alpha and the one patient with alpha-5nt alpha/alpha-5nt alpha indicates the presence of minute amounts of alpha 2-mRNA; apparently splicing at the donor site is greatly impaired by this deletion but not eliminated. The high alpha 2/alpha 1-mRNA ratio in the four patients with - -/alpha PA-2 alpha and the five patients with alpha PA-1 alpha/ alpha PA-1 alpha (PA-1 and PA-2 are poly(A) mutations) is due to the presence of an elongated alpha 2-mRNA which uses an alternate location as polyadenylation site. The relative levels zeta-mRNA varied considerably; the highest levels were found in patients with the -(alpha)20.5/-alpha or - -SEA/-alpha deletional types but not in those with the -(alpha)20.5/alphaPA-2 alpha, -(alpha)20.5/alpha-5nt alpha, or - -SEA/alphaCS alpha nondeletional types. No definitive explanation can be given for these differences; perhaps certain sequences that are part of some of the alpha-thal-1 deletions are important for the suppression of the zeta-globin gene.

Adolescent↗

PubMed1992

Type I human complement C2 deficiency. A 28-base pair gene deletion causes skipping of exon 6 during RNA splicing.

Two variants of a genetic deficiency of complement protein C2 (C2D) have been previously identified. No C2 protein translation is detected in type I deficiency, while type II deficiency is characterized by a selective block in C2 secretion. Type I C2 deficiency was described in a family in which the C2 null allele (C2Q0) is associated with the major histocompatibility haplotype/complotype HLA-A25,B18,C2Q0,BfS,C4A4, C4B2,Drw2; this extended haplotype occurs in over 90% of C2-deficient individuals (common complotype/haplotype). To determine the molecular basis of type I C2 deficiency, the C2 gene and cDNA were characterized from a homozygous type I C2-deficient individual with the common associated haplotype/complotype. We found a 28-base pair deletion in the type I C2Q0 gene, beginning 9 base pairs upstream of the 3'-end of exon 6, that generates a C2 transcript with a complete deletion of exon 6 (134 base pair) and a premature termination codon. In studies of eight kindred, the 28-base pair deletion was observed in all C2Q0 alleles associated with the common type I deficient complotype/haplotype; this deletion was not present in normal C2 nor in type II C2-deficient genes. These data demonstrate that: 1) type I human complement C2 deficiency is caused by a 28-base pair genomic deletion that causes skipping of exon 6 during RNA splicing, resulting in generation of a premature termination codon, 2) the 28-base pair deletion in the type I C2Q0 gene is strongly associated with the HLA haplotype/complotype A25,B18,C2Q0,BfS,C4A4,C4B2,Drw2, suggesting that all C2-deficient individuals with this haplotype/complotype will harbor the 28-base pair C2 gene deletion, and 3) type II C2 deficiency is caused by a different, as yet uncharacterized, molecular genetic defect.

Amino Acid Sequence↗

PubMed2000

The accuracy of codon recognition by polypeptide release factors.

The precision with which individual termination codons in mRNA are recognized by protein release factors (RFs) has been measured and compared with the decoding of sense codons by tRNA. An Escherichia coli system for protein synthesis in vitro with purified components was used to study the accuracy of termination by RF1 and RF2 in the presence or absence of RF3. The efficiency of factor-dependent termination at all sense codons differing from any of the three stop codons by a single mutation was measured and compared with the efficiency of termination at the three stop codons. RF1 and RF2 discriminate against sense codons related to stop codons by between 3 and more than 6 orders of magnitude. This high level of accuracy is obtained without energy-driven error correction (proofreading), in contrast to codon-dependent aminoacyl-tRNA recognition by ribosomes. Two codons, UAU and UGG, stand out as hotspots for RF-dependent premature termination.

Codon, Terminator↗

PubMed1998

Nonstructural protein-2 and the replication of canine parvovirus.

The nonstructural protein-2 (NS2) of canine parvovirus (CPV) is produced from the left-hand open reading frame of the viral genome and contains 87 amino-terminal amino acids in common with nonstructural protein 1 (NS1) joined to 78 amino acids from an alternative open reading frame. In the minute virus of mice parvovirus NS2 plays a role in controlling capsid protein assembly and translation in a host-specific manner. The predicted NS2 of CPV is divergent from the proteins of the rodent parvoviruses, and the protein and its functions have not been described. We characterized the large and the small splices of CPV using reverse transcriptase-PCR, NS2 was identified using anti-peptide antibodies against the predicted C-terminal sequence and also by expressing the protein from a plasmid vector. The protein could be detected at low levels in the nucleus and the cytoplasm of a proportion of CPV-infected cells, as well as in cells transfected with the expression plasmid. Virus genomes were prepared with mutations in the splice donor or acceptor sites of the NS2-specific intron or with three different termination codons in the NS2-unique exon. Both splice donor and acceptor mutations resulted in the use of previously cryptic splice sites, and the virus containing the splice donor mutation replicated inefficiently. However, the other four mutant viruses were all viable and replicated efficiently in cat and dog cells, and two mutant viruses that were tested appeared to assemble their capsids in the same manner as did the wildtype. After inoculation of dogs an NS2 mutant virus with a termination codon in the NS2-unique exon replicated to titers similar to those seen for wildtype CPV in several tissues examined.

Alternative Splicing↗

PubMed2000

Engineering EGFP reporter constructs into a 200 kb human beta-globin BAC clone using GET Recombination.

GET Recombination, a simple inducible homologous recombination system for Escherichia coli, was used to target insertion of an EGFP cassette between the start and termination codons of the beta-globin gene in a 200 kb BAC clone. The high degree of homology between the promoter regions of the beta- and delta-globin genes also allowed the simultaneous generation of a delta-globin reporter construct with the deletion of 8.8 kb of intervening sequences. Both constructs expressed EGFP after transient transfection of MEL cells. Similarly, targeting of the EGFP cassette between the promoter regions of the gamma-globin genes and the termination codon of the beta-globin gene enabled the generation of reporter constructs for both (A)gamma- and (G)gamma-globin genes, involving specific deletions of 24 and 29 kb of genomic sequence, respectively. Finally the EGFP cassette was also inserted between the epsilon- and beta-globin genes, with the simultaneous deletion of 44 kb of intervening sequence. The modified constructs were generated at high efficiency, illustrating the usefulness of GET Recombination to generate large deletions of specific sequences in BACs for functional studies. The establishment of stable erythropoietic cell lines with these globin constructs will facilitate the search for therapeutic agents that modify the expression of the individual globin genes in a physiologically relevant manner.

Cloning, Molecular↗

PubMed2004

Nonsense-mediated decay approaches the clinic.

Nonsense-mediated decay (NMD) eliminates mRNAs containing premature termination codons and thus helps limit the synthesis of abnormal proteins. New results uncover a broader role of NMD as a pathway that also affects the expression of wild-type genes and alternative-splice products. Because the mechanisms by which NMD operates have received much attention, we discuss here the emerging awareness of the impact of NMD on the manifestation of human genetic diseases. We explore how an understanding of NMD accounts for phenotypic differences in diseases caused by premature termination codons. Specifically, we consider how the protective function of NMD sometimes benefits heterozygous carriers and, in contrast, sometimes contributes to a clinical picture of protein deficiency by inhibiting expression of partially functional proteins. Potential 'NMD therapeutics' will therefore need to strike a balance between the general physiological benefits of NMD and its detrimental effects in cases of specific genetic mutations.

Alternative Splicing↗