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PubMed1995

Functional characterization of the 180-kD ribosome receptor in vivo.

A cDNA encoding the 180-kD canine ribosome receptor (RRp) was cloned and sequenced. The deduced primary structure indicates three distinct domains: an NH2-terminal stretch of 28 uncharged amino acids representing the membrane anchor, a basic region (pI = 10.74) comprising the remainder of the NH2-terminal half and an acidic COOH-terminal half (pI = 4.99). The most striking feature of the amino acid sequence is a 10-amino acid consensus motif, NQGKKAEGAP, repeated 54 times in tandem without interruption in the NH2-terminal positively charged region. We postulate that this repeated sequence represents a ribosome binding domain which mediates the interaction between the ribosome and the ER membrane. To substantiate this hypothesis, recombinant full-length ribosome receptor and two truncated versions of this protein, one lacking the potential ribosome binding domain, and one lacking the COOH terminus, were expressed in Saccharomyces cerevisiae. Morphological and biochemical analyses showed all proteins were targeted to, and oriented correctly in the ER membrane. In vitro ribosome binding assays demonstrated that yeast microsomes containing the full-length canine receptor or one lacking the COOH-terminal domain were able to bind two to four times as many human ribosomes as control membranes lacking a recombinant protein or microsomes containing a receptor lacking the NH2-terminal basic domain. Electron micrographs of these cells revealed that the expression of all receptor constructs led to a proliferation of perinuclear ER membranes known as "karmellae." Strikingly, in those strains which expressed cDNAs encoding a receptor containing the putative ribosome binding domain, the induced ER membranes (examined in situ) were richly studded with ribosomes. In contrast, karmellae resulting from the expression of receptor cDNA lacking the putative ribosome binding domain were uniformly smooth and free of ribosomes. Cell fractionation and biochemical analyses corroborated the morphological characterization. Taken together these data provide further evidence that RRp functions as a ribosome receptor in vitro, provide new evidence indicating its functionality in vivo, and in both cases indicate that the NH2-terminal basic domain is essential for ribosome binding.

Amino Acid Sequence↗
PubMed1995

The refractory period after eucapnic voluntary hyperventilation challenge and its effect on challenge technique.

To evaluate whether there is a refractory period (RP) after hyperventilation challenge, we compared the bronchoconstrictive response to repetitive eucapnic voluntary hyperventilation challenge with dry, room temperature air (EVH). The serial challenges were identical with 11 known asthmatics hyperventilating for 6 min at a target minute ventilation of 30 times their FEV1 measured before either challenge. There was a significant difference between the mean postchallenge fall in FEV1 to the initial EVH challenge (27.4 +/- 9.8%) and the response to the second EVH challenge (16.1 +/- 5.9%) (p = 0.0001), indicating refractoriness. We then evaluated whether 6 min of uninterrupted EVH challenge gives a similar bronchospastic response to that which results from an equivalent (by total minute ventilation) interrupted challenge of 2 min of EVH repeated three times. The mean post-challenge fall in FEV1 in response to this interrupted challenge was 18.9 +/- 10.6%, which was significantly different from the 27.4% fall in response to 6 consecutive minutes of EVH (p = 0.036). This study demonstrates that there is a refractory period after repeated EVH challenges and this refractoriness affects the response to interrupted, or dosed, EVH challenge.

Adult↗
PubMed2000

Identification and characterization of the miniature pig Huntington's disease gene homolog: evidence for conservation and polymorphism in the CAG triplet repeat.

Huntington's disease (HD) is associated with a significant expansion of a CAG trinucleotide repeat, which results in a lengthened polyglutamine tract in the single gene product, huntingtin, on human 4p16.3. We isolated cDNA clones that encompassed the entire coding sequence of the miniature pig HD gene (Sus HD) from two porcine testis cDNA libraries. The cDNA contig revealed a 12,749-nucleotide transcript coding for a 345-kDa protein (3139 amino acid residues), which exhibited 96% peptide sequence homology to human huntingtin. Northern blot analysis revealed that the Sus HD gene was ubiquitously expressed as two large transcripts of approximately 11 and 13 kb in size in all the tested tissues, much like the human HD gene. The CAG trinucleotide repeat was found to be interrupted by CAA triplets and to encode 17 or 18 consecutive glutamine residues. In our laboratory stock of miniature pig, three allotypes in the triplet repeat sequence were found. Thus, the Sus HD gene closely resembles its human counterpart in terms of sequence and expression pattern. In particular, human-miniature pig similarities in the normal length of the CAG triplet repeat as well as its repeat-number polymorphism may indicate that miniature pig would provide a good animal model for Huntington's disease.

3' Untranslated Regions↗
PubMed1995

Evolution of the cryptic FMR1 CGG repeat.

We have sequenced the 5' untranslated region of the orthologous FMR1 gene from 44 species of mammals. The CGG repeat is present in each species, suggesting conservation of the repeat over 150 million years of mammalian radiation. Most mammals possess small contiguous repeats (mean number of repeats = 8.0 +/- 0.8), but in primates, the repeats are larger (mean = 20.0 +/- 2.3) and more highly interrupted. Parsimony analysis predicts that enlargement of the FMR1 CGG repeat beyond 20 triplets has occurred in three different primate lineages. In man and gorilla, AGG interruptions occur with higher-order periodicity, suggesting that historical enlargement has involved incremental and vectorial addition of larger arrays demarcated by an interruption. Our data suggest that replication slippage and unequal crossing over have been operative during the evolution of this repeat.

Animals↗
PubMed1999

Repeat noninvasive bladder pressure measurements with an external catheter.

PURPOSE: Previously it has been shown that an objective diagnosis of infravesical obstruction can be made by combining the maximum flow rate and isovolumetric bladder pressure. We evaluate a noninvasive method to measure isovolumetric bladder pressure to help develop a noninvasive modality for diagnosing obstruction. MATERIALS AND METHODS: An external catheter consisting of an incontinence condom, tube and pressure transducer was used. Flow rate through the catheter was remotely interrupted to measure the bladder pressure in the condom. Two series of measurements were done in 11 healthy male volunteers. In the first series we determined whether voiding was affected after flow rate interruption. In the second series we analyzed repeat pressure measurements of 1 voiding to determine whether maximum isovolumetric pressure depended on bladder volume. RESULTS: Flow rate was unaffected after interruption for pressure measurement. Repeat measurements of isovolumetric bladder pressure demonstrated that the pressure depended significantly on bladder volume. Average maximum isovolumetric pressure was 12.2 kPa. at a bladder volume of 251 ml. CONCLUSIONS: As no inhibition of voiding was noted after a single pressure measurement, repeat noninvasive measurements can be made on voiding. With repeat measurements the dependence of isovolumetric bladder pressure on bladder volume can be considered to obtain a reliable estimate of pressure as a basis for a noninvasive diagnosis of obstruction.

Adult↗
PubMed2001

Analysis of FMR1 (CGG)(n) alleles and DXS548-FRAXAC1 haplotypes in three European circumpolar populations: traces of genetic relationship with Asia.

Fragile X syndrome, the most common form of inherited mental retardation, is caused by expansion of a (CGG)(n) repeat located in the FMR1 gene. The molecular factors involved in the mutation process from stable (CGG)(n) alleles towards unstable alleles are largely unknown, although family transmission studies and population studies have suggested that loss of AGG interruptions in the (CGG)(n) repeat is essential. We have analysed the AGG interspersion pattern of the FMR1 (CGG)(n) repeat and the haplotype distribution of closely located microsatellite markers DXS548 and FRAXAC1, in three circumarctic populations: Norwegians, Nenets and Saami. The data confirm the conservation, reported in all human populations studied so far, of an AGG interruption for each 9-10 CGG and support the stabilising effect of AGG interruptions. The data also indicate the existence of chromosomes of Asian origin in the Saami and Nenets population, thereby confirming a genetic relationship between Northern Europe and Asia. DXS548-FRAXAC1 haplotype frequencies were compared between 24 Norwegian fragile X males and 119 normal males. Significant linkage disequilibrium were found between the fragile X mutation and haplotype 6-4 and between normal (CGG)(n) alleles and haplotype 7-3.

Alleles↗
PubMed1996

Primate origin of the CMT1A-REP repeat and analysis of a putative transposon-associated recombinational hotspot.

The CMT1A-REP repeat on chromosome 17p11.2-12 is proposed to mediate misalignment and meiotic unequal crossover leading to a 1.5 Mb pair duplication associated with Charcot-Marie-Tooth neuropathy type 1A (CMT1A) and a reciprocal deletion associated with hereditary neuropathy with liability to pressure palsies (HNPP). Restriction enzyme endonuclease mapping indicated that the size of the CMT1A-REP repeat is approximately 24 kb and DNA sequence analysis determined that the repeat is flanked by inverted Alu sequences. Full length Alu sequences are present at the centromeric ends of the proximal and distal CMT1A-REP repeats and at the telomeric end of the distal repeat. A truncated Alu sequence is present at the telomeric end of the proximal repeat suggesting that the distal CMT1A-REP repeat is the progenitor copy. The crossover breakpoints for a series of unrelated CMT1A and HNPP patients were mapped using a variant SacI site found only in the proximal CMT1A-REP repeat. Seventy-six percent (66/85) of patients had breakpoints which mapped to a 3.2 kb interval, providing further evidence for a recombinational hotspot within the CMT1A-REP repeat. A mariner-like element was mapped within the CMT1A-REP repeat approximately 700 bp centromeric to the 3.2 kb interval containing the hotspot. Analysis of this sequence suggested that it does not encode a functional transposon. By Northern blot analysis a cloned fragment from the CMT1A-REP repeat containing the mariner-like sequence detected a 2.2 kb transcript only in testis. Two cDNA clones which contain the mariner-like element were isolated from a human testis cDNA library. These clones which are interrupted by Alu and other repeats appear to be non-functional versions of the transposon. The functional relationship of the mariner-like element to the recombinational hotspot remains unknown. The origin of the CMT1A-REP repeat was investigated through an analysis of homologous sequences in non-human primates. Southern blot analysis indicated that the chimpanzee has two copies of a CMT1A-REP-like sequence, whereas gorilla, orangutan, and gibbon have a single copy. A high degree of conservation amongst non-human primates for restriction fragments specific to the human distal CMT1A-REP repeat provides further evidence that the distal repeat is the progenitor copy. The mariner-like sequence was detected in association with the CMT1A-REP sequence in all primates studied suggesting that the mariner-like element was introduced into the progenitor CMT1A-REP sequence prior to emergence of the proximal and distal CMT1A-REP repeats. These observations suggest that CMT1A-REP sequence appeared as a repeat before the divergence of chimpanzee and human, but after gorilla and human around 6 to 7 million years ago.

Animals↗
PubMed2004

Replication-mediated instability of the GAA triplet repeat mutation in Friedreich ataxia.

Friedreich ataxia is caused by the expansion of a polymorphic and unstable GAA triplet repeat in the FRDA gene, but the mechanisms for its instability are poorly understood. Replication of (GAA*TTC)n sequences (9-105 triplets) in plasmids propagated in Escherichia coli displayed length- and orientation-dependent instability. There were small length variations upon replication in both orientations, but large contractions were frequently observed when GAA was the lagging strand template. DNA replication was also significantly slower in this orientation. To evaluate the physiological relevance of our findings, we analyzed peripheral leukocytes from human subjects carrying repeats of similar length (8-107 triplets). Analysis of 9400 somatic FRDA molecules using small-pool PCR revealed a similar mutational spectrum, including large contractions. The threshold length for the initiation of somatic instability in vivo was between 40 and 44 triplets, corresponding to the length of a eukaryotic Okazaki fragment. Consistent with the stabilization of premutation alleles during germline transmission, we also found that instability of somatic cells in vivo and repeats propagated in E.coli were abrogated by (GAGGAA)n hexanucleotide interruptions. Our data demonstrate that the GAA triplet repeat mutation in Friedreich ataxia is destabilized, frequently undergoing large contractions, during DNA replication.

DNA↗
PubMed1981

Ribosomal insertion-like elements in Drosophila melanogaster are interspersed with mobile sequences.

Sequences homologous to the type 1 ribosomal DNA insertion occur in the chromocenter and in one location on the fourth chromosome of Drosophila melanogaster. Ribosomal insertion-like elements frequently occur in the form of tandem repeats and are often interspersed with nonhomologous DNA. Sequences that interrupt of flank insertion-like elements are members of diverged repeated DNA families. Members of five of these interspersed sequence families are located at multiple euchromatic sites as well as in the chromocenter. The euchromatic sites differ greatly in the gt-1 and gt-X11 stocks of D. melanogaster, suggesting that these sequence families are mobile in the genome. No long inverted repeats were detected in any of these interspersed sequences. One sequence, called 101F, interrupts a ribosomal insertion-like element; the nucleotide sequences across the boundaries between 101F and ribosomal insertion have been determined. A stretch of 13 base pairs that is present once in the ribosomal insertion is repeated at the ends of the 101F sequence, suggesting a target site duplication. Within the 101F element, no extended direct or inverted repeat sequence exists. The interspersed repeated sequences studied are transcribed into rare, heterogeneous, poly(A)-lacking nuclear RNA molecules. In one case, we showed that both strands of a flanking sequence are transcribed, but to a different extent. With respect to structural features and the nature of their transcripts, the sequences described here are distinct from other known transposable elements in Drosophila.

Animals↗
PubMed1999

Peptide models for inherited neurodegenerative disorders: conformation and aggregation properties of long polyglutamine peptides with and without interruptions.

Several neurodegenerative diseases are caused by expansion of polyglutamine repeats in the affected proteins. In spino-cerebellar ataxia type 1 (SCA1), histidine interruptions have been reported to mitigate the pathological effects of long glutamine stretches. To understand this phenomenon, we investigated the conformational preferences of peptides containing both the uninterrupted polyglutamine stretches and those with histidine interruption(s) as seen in SCA1 normals. Our study suggests that substitution of histidines by glutamines induces a conformational change which results in decreased solubility and increased aggregation. Our findings also suggest that all the polyglutamine peptides with and without interruption(s) adopt a beta-structure and not random coil.

Ataxin-1↗
PubMed1993

Opa-like repeats in the genome of the Medfly Ceratitis capitata.

The sequence determination of several genomic clones isolated from the Mediterranean fruitfly Ceratitis capitata identified the existence of opa-like repeats, often more than one being clustered in small chromosomal segments. These repeats have previously been shown to consist of stretches of tandemly reiterated glutamine-encoding residues, and they are found in multiple genes of several organisms. Most of the repeats described here are flanked or interrupted by stop codons in all reading frames and, thus, could not possibly be part of protein-coding sequences. Furthermore, these repeats, of which there are several hundred in the genome of the Medfly, can be used effectively for the determination of sequence polymorphisms, providing a convenient approach to obtain additional landmarks for the construction of genomic maps of this economically important insect.

Amino Acid Sequence↗
PubMed1988

A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60.

A 50-nucleotide untranslated region is shown to be present within the coding sequence of Escherichia coli bacteriophage T4 gene 60, which encodes one of the subunits for its type II DNA topoisomerase. This interruption is part of the transcribed messenger RNA and appears not to be removed before translation. Thus, the usual colinearity between messenger RNA and the encoded protein sequence apparently does not exist in this case. The interruption is bracketed by a direct repeat of five base pairs. A mechanism is proposed in which folding of the untranslated region brings together codons separated by the interruption so that the elongating ribosome may skip the 50 nucleotides during translation. The alternative possibility, that the protein is efficiently translated from a very minor and undetectable form of processed messenger RNA, seems unlikely, but has not been completely ruled out.

Amino Acid Sequence↗
PubMed1995

The stabilization of repetitive tracts of DNA by variant repeats requires a functional DNA mismatch repair system.

Simple repetitive tracts of DNA are unstable in all organisms thus far examined. In the yeast S. cerevisiae, we show that a 51 bp poly(GT) tract alters length at a rate of about 10(-5) per cell division. Insertion of a single variant repeat (either AT or CT) into the middle of the poly(GT) tract results in 100-fold stabilization. This stabilization requires the DNA mismatch repair system. Alterations within tracts with variant repeats occur more frequently on one side of the interruption than on the other. The stabilizing effects of variant repeats and polarity of repeat alterations have also been observed in trinucleotide repeats associated with certain human diseases.

Base Sequence↗
PubMed1999

Interrupter technique for evaluation of exercise-induced bronchospasm in children.

The free running test is a useful method for evaluation of exercise-induced bronchospasm in children. In young children this test simulates real-life circumstances and can be done more easily than histamine or methacholine challenges. The interrupter technique is a noninvasive method for measuring airflow resistance during tidal breathing. This approach requires minimal cooperation, and is therefore promising for use in young children. Fifty children aged 5-15 years with asthma symptoms were tested by exercise challenge consisting of free outdoor running for 8 min at 85% of maximal predicted heart rate for age. Pulmonary function was measured by using the interrupter technique (IR), with a Wright's peak flow meter (WPEF), and by flow-volume spirometry (FVS). The measurements were done before and 10 min after exercise. In addition, WPEF was measured at 5, 15, and 20 min after exercise. A fall of 15% or more in WPEF associated with wheezing or cough symptoms was considered a positive test. The exercise challenge was positive in 16 (32%) of the 50 children. Measurements at 10 min by WPEF identified 9 positive cases. At the same time point the IR identified 10 positive cases; a rise in resistance of 15% or more was considered positive, giving it 80% sensitivity and 93% specificity. The repeatability coefficient (CoR) for the interrupter technique was 0.06 kPa x L(-1) x s (13%) before and 0.07 kPa x L(-1) x s (14%) after exercise. The IR provides a useful alternative for estimation of airway obstruction in children following exercise challenge. The results were comparable with the current reference methods of forced expiratory volume in 1 s and peak flow measurements.

Adolescent↗
PubMed1992

Cloning and developmental expression of the alpha 3 chain of chicken type IX collagen.

Fibrous and nonfibrous collagens comprise two major groups within the collagen family and both groups are found in a diverse variety of tissue fabrics. Type IX collagen is in the nonfibrous group; three different subunits of type IX collagen have been identified and the alpha 1 and alpha 2 subunits have been cloned. Using molecular cloning methods we have isolated, from an embryonic chicken cartilage library, cDNA clones which code for the entire alpha 3 chain of chicken type IX collagen. The cDNA clones encompass 2416 base pairs which have a conceptual open reading frame for a protein containing 675 amino acids including 193 Gly-X-Y repeats. These collagen repeats are in three separate domains which are interspersed with four major noncollagen domains. The collagen repeats also have four minor interruptions. This chain organization directly aligns with both the alpha 1 and alpha 2 chains of chicken type IX collagen. Comparison of the deduced amino acid sequence with peptide sequences of type IX collagens shows identity with 95 of the 96 known residues of the chicken alpha 3 chain and 81 of the 98 known residues of the bovine alpha 3 chain. The identical residues match those in five peptide fragments, two from the bovine protein and three from the chicken protein. The chicken and bovine alpha 3 chains have conserved cross-linking sites, separated by 137 residues which span 40 nm, the length of the hole zone in a collagen fibril. The NC3 domain of the chicken alpha 3 chain contains a repeat Cys-Pro motif which is present in both vertebrate and invertebrate nonfibrillar collagens. Northern blot hybridization exhibits a major mRNA of about 3.3 kilobases; this transcript is found in cartilaginous tissues in the embryo, including the developing limb and is not detected in other tissues or in the precondensation stage of limb development. The composite data delineate the primary structure of the alpha 3 chain of chicken type IX collagen, show its close relationship to the alpha 1 and alpha 2 chains, demonstrate its mRNA transcript, and show the appearance of that transcript in tissues of the developing chick embryo.

Amino Acid Sequence↗
PubMed2006

CAG*CTG repeat instability in cultured human astrocytes.

Cells of the central nervous system (CNS) are prone to the devastating consequences of trinucleotide repeat (TNR) expansion. Some CNS cells, including astrocytes, show substantial TNR instability in affected individuals. Since astrocyte enrichment occurs in brain regions sensitive to neurodegeneration and somatic TNR instability, immortalized SVG-A astrocytes were used as an ex vivo model to mimic TNR mutagenesis. Cultured astrocytes produced frequent (up to 2%) CAG.CTG contractions in a sequence-specific fashion, and an apparent threshold for instability was observed between 25 and 33 repeats. These results suggest that cultured astrocytes recapitulate key features of TNR mutagenesis. Furthermore, contractions were influenced by DNA replication through the repeat, suggesting that instability can arise by replication-based mechanisms in these cells. This is a crucial mechanistic point, since astrocytes in the CNS retain proliferative capacity throughout life and could be vulnerable to replication-mediated TNR instability. The presence of interruptions led to smaller but more frequent contractions, compared to a pure repeat, and the interruptions were sometimes deleted to form a perfect tract. In summary, we suggest that CAG.CTG repeat instability in cultured astrocytes is dynamic and replication-driven, suggesting that TNR mutagenesis may be influenced by the proliferative capacity of key CNS cells.

Alleles↗
PubMed1980

The 10 kb Drosophila virilis 28S rDNA intervening sequence is flanked by a direct repeat of 14 base pairs of coding sequence.

Most repeat units of rDNA in Drosophila virilis are interrupted in the 28S rRNA coding region by an intervening sequence about 10 kb in length; uninterrupted repeats have a length of about 11 kb. We have sequenced the coding/intervening sequence junctions and flanking regions in two independent clones of interrupted rDNA, and the corresponding 28S rRNA coding region in a clone of uninterrupted rDNA. The intervening sequence is terminated at both ends by a direct repeat of a fourteen nucleotide sequence that is present once in the corresponding region of an intact gene. This is a phenomenon associated with transposable elements in other eukaryotes and in prokaryotes, and the Drosophila rDNA intervening sequence is discussed in this context. We have compared more than 200 nucleotides of the D. virilis 28S rRNA gene with sequences of homologous regions of rDNA in Tetrahymena pigmentosa (Wild and Sommer, 1980) and Xenopus laevis (Gourse and Gerbi, 1980): There is 93% sequence homology among the diverse species, so that the rDNA region in question (about two-thirds of the way into the 28S rRNA coding sequence) has been very highly conserved in eukaryote evolution. The intervening sequence in T. pigmentosa is at a site 79 nucleotides upstream from the insertion site of the Drosophila intervening sequence.

Animals↗
PubMed1997

Characterization of an abundant, unique 1.7-kilobase bovine herpesvirus 4 (BHV-4) late RNA and mapping of a BHV-4 IE2 transactivator-binding site in its promoter-regulatory region.

We characterized an abundant late 1.7-kb cytoplasmic polyadenylated RNA (L1.7 RNA) transcribed from the bovine herpesvirus 4 (BHV-4) HindIII W fragment, in a region of the genome not conserved with Epstein-Barr virus and herpesvirus saimiri. L1.7 RNA contains only extremely short (<100 nucleotides) open reading frames followed by two repeat arrays. The first repeat array contains 11 copies of a 23-bp unit, TGGCACTA GTAGCATTTAACCCC. The second and third copies are each interrupted by 15- to 17-bp sequences that are identical to each other for the first 15 bp. In addition, the second and third copies of the repeat unit each contain two copies of nucleotides 5 to 9 (ACTAG) of the repeat unit, one at each end of the interruption. The second repeat array contains 12 copies of a 25-bp sequence, GCTGTGTATTATTGAGTATTTTTTA. The promoter-regulatory region of L1.7 was activated by the BHV-4 immediate-early gene 2 product (IE2), a homolog of the Epstein-Barr virus R transactivator, in cotransfection assays. We mapped an IE2 recognition site within a 167-bp fragment approximately 10 bp 5' to the start of L1.7 RNA transcription, using cotransfection assays and gel retardation assays. Using gel retardation assays, we mapped an IE2-binding site within this fragment to a 31-bp region from 56 to 86 bp 5' to the start of L1.7 RNA transcription. This IE2-binding site was able to transfer IE2 responsiveness to a heterologous promoter. However, IE2 responsiveness was affected by both position and orientation. Alignment of the L1.7 IE2-binding site sequence with sequences of two other BHV-4 IE2-binding sites resulted in a provisional IE2-binding site consensus sequence different from the Epstein-Barr virus R transactivator-binding site.

Animals↗