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Results for “insertion, inversion”

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PubMed1996

The role of charged residues in determining transmembrane protein insertion orientation in yeast.

The first 79 residues of the yeast Ste2p G protein-coupled pheromone receptor, including the negatively charged N-terminal domain, the first transmembrane segment, and the following positively charged cytoplasmic loop, has been fused to a Kex2p-cleavable beta-lactamase reporter. Insertion orientation was determined by analysis of cell-associated and secreted beta-lactamase activities and independently corroborated by analysis of membrane association and glycosylation patterns. This fusion inserts with exclusively N terminus exofacial (Nexo) topology, serving as a model type III membrane protein. Orientation is unaffected by removal of all three positively charged residues in the cytoplasmic loop or by deletion of all but 12 residues from the N-terminal domain. The residual -2 N-terminal charge apparently provides a signal sufficient to determine Nexo topology. This is entirely consistent with the statistically derived rule in which the charge difference, Delta(C-N), counted for the 15 immediately flanking residues, is the primary topology determinant. Mutations altering Delta(C-N) to zero favors Nexo insertion by 3 to 1, whereas increasingly negative values cause increasing inversion of orientation. All results are consistent with the charge difference rule and indicate that whereas positive charges promote cytoplasmic retention, negative charges promote translocation.

Amino Acid Sequence↗

PubMed2006

Genetic determinants of capsular serotype K1 of Klebsiella pneumoniae causing primary pyogenic liver abscess.

BACKGROUND: Primary pyogenic liver abscess (PLA) caused by Klebsiella pneumoniae is an emerging infectious disease. Capsular serotype K1 and the magA gene have been reported to be associated with this disease. METHODS: The prevalence of magA was determined by polymerase chain reaction (PCR). The sequences of the magA flanking region were completed by inverse PCR and direct sequencing. Serotyping was performed by double immunodiffusion. Insertion mutations and trans-complementation were used to define the K1 genetic determination region. RESULTS: Thirty-five of 42 strains from patients with PLA were magA positive, whereas only 1 of 32 non-PLA strains was magA positive. All 36 magA-positive strains were serotype K1, and the 38 magA-negative strains were not (36/36 vs. 0/38; P<.0001). Sequencing of the magA flanking region revealed a putative capsular polysaccharide synthesis (cps) region; this region was 25 kb in length and contained 20 open reading frames (ORFs); of these ORFs, 9 were cotranscribed as part of an operon and differed from both MGH78578 and the Chedid strain. Mutation of 4 genes in this region turned the mutant strains anti-K1 negative. Trans-complementation restored the K1 phenotype. CONCLUSIONS: The operon containing magA is responsible for capsular serotype K1 of K. pneumoniae. Several loci in the operon are unique determinants of K1 strains.

Antigens, Bacterial↗

PubMed2002

Molecular cloning of a gene for inversion of embryo turning (inv) with cystic kidney.

Vertebrate internal organs of the body develop with a distinctive left-right asymmetry. The mouse inversion of embryonic turning (inv) mutation which was created by random insertional mutagenesis causes a constant reversal of the left-right polarity (situs inversus) as well as cyst formation in the kidney in homozygotes. Since this phenotype is tightly linked to the transgenic integration site, the disrupted gene is likely to be located near this site. To analyse the transgenic integration site, ICRF yeast artificial chromosome (YAC) clones were screened by hybridization with a probe containing this site. Three positive YACs were identified and cosmid libraries were constructed from these. The insertional mutagenesis created a 60 kb genomic deletion on mouse chromosome 4. A cosmid contig spanning the whole deleted region was generated by genomic walking. In an effort to identify transcript(s), we used cosmid insert DNA to screen mouse embryo cDNA libraries directly after pre-competition with Cot1 DNA to suppress the non-specific signal. Only one cDNA clone (3 kb, clone 28) was identified, and we then obtained full-length cDNA. Genomic Southern hybridization indicated that this gene spans the whole deleted region, implying that the homozygous inv mice have an intragenic deletion of this gene. Northern hybridization showed that the gene is expressed as early as embryonic day 7, and its size was approximately 5.6 kb. As the highest expression is seen in kidney and liver in the adult, the expression patterns are consistent with our postulate that the gene is responsible not only for reversal of left-right asymmetry but also for cyst formation in the kidney in the inv mutant. The deduced amino acid sequence shows that the gene has 15 successive repeats of an Ank/Swi6 motif in its N-terminal domain. These repeats are considered to provide a mechanism for recognition of proteins, such as to fix target proteins at certain cellular locations or alter intracellular location of target binding proteins. In conclusion, we have cloned an inv candidate gene that is responsible for both the situs inversus and cyst-forming kidney. The gene product involves ankyrin motif repeats, indicating that a cytoskeleton disruption induces the situs inversus and the cystic kidney.

Animals↗

PubMed1982

The case for modulated parasystole.

Several recently published tracings of parasystolic rhythms with unusual features were studied to determine whether the biphasic response curve characteristic of modulated parasystole could be extracted from the patterns of arrhythmia. Even in cases in which the possibility of modulation had been rejected, the phase response curves could be derived by inverse analysis of the ectopic intervals. When the derived curves were inserted into the program of the computer model, almost exact matches for the clinical patterns were recorded. In one case, in which the right atrium was driven at increasing rates, the patterns of manifest ectopic ventricular responses appeared to be re-entrant rather than parasystolic. In this case, similar patterns as a function of heart rate were recorded from a mathematical model of reflection.

Arrhythmias, Cardiac↗

PubMed1984

Human smooth and saccadic eye movements during voluntary pursuit of different target motions on different backgrounds.

Horizontal and vertical eye movements of ten human subjects were recorded with a scleral induction-coil technique during voluntary pursuit of sinusoidal, triangular and pseudo-random target motions of different frequency, amplitude and dimensionality upon a dark, diffuse or structured background. Data processing included separation of the composite eye movement into a cumulative smooth and saccadic displacement, computation of gain and phase of the composite and smooth eye movements with respect to the target movement and analysis of retinal position error. Pursuit eye movements were never completely smooth. Smooth pursuit gain was always lower than 0.95 and saccades were used to supplement the smooth eye movements in pursuing the target with the proper amplitude. The gain of composite eye movements was about unity for sinusoidal target motions and ramps; it exceeded unity for the highest frequency components in a pseudo-random motion. The gain of the smooth eye movements decreased monotonously whenever target velocity increased. It was higher for single sine waves than for a pseudo-random motion, however, with pseudo-random motion it was relatively higher for the higher frequency components. Phase lags were in general smaller for single sine waves than for pseudo-random motion, but for the latter a phase lead of the smooth component was consistently found for the lower frequency components. During pursuit of a rhomboid trajectory, the eye movements showed directional errors which are interpreted as anticipatory behaviour. The distribution of the retinal error was symmetrical around zero. Its standard deviation varied between about 0.2 and 1.3 degrees; it was about proportional to target velocity and inversely proportional to smooth pursuit gain. It was limited by the insertion of saccades which were in general corrective. The influence of a diffusely illuminated background was minimal. A structured background inhibited smooth pursuit in the horizontal direction by about 10% and in the vertical direction by about 20%. This deficit of smooth pursuit was fully compensated by the insertion of more saccades and had no consequences for the standard deviation of the retinal error. The type of structure of the background was only of marginal importance. Horizontal pursuit was in general slightly smoother and more precise than vertical pursuit.

Adult↗

PubMed2000

Limits of a deletion spanning Tlr4 in C57BL/10ScCr mice.

Proceeding from our observation that LPS-unresponsive mice of the strain C57BL/10ScCr mice fail to express the Tlr4 gene [Poltorak A, He X. Smirnova I et al. Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science 1998; 282: 2085], we have defined the exact limits of a deletion encompassing Tlr4 in the C57BL/10ScCr genome. The deletion removes 74723 bp of DNA, with reference to the control strain 129/J (from which the complete sequence of the Tlr4 locus was obtained). There is no inserted element, and no re-arrangement of the chromosome (e.g. inversion or translocation) in the immediate region of Tlr4; the deletion removes only one recognizable gene. Hence, other immunological anomalies that have been identified in C57BL/10ScCr mice (a non-healing phenotype in Leishmania inoculation and failure to produce interferon-gamma in response to numerous microbial infections) must be ascribed to one of two causes. Mutation(s) at other loci may be responsible for these defects. Alternatively, Tlr4 locus deletion may have phenotypic consequences that exceed the well known blockade of LPS signal transduction.

Animals↗

PubMed2006

Variations in gene organization and DNA uptake signal sequence in the folP region between commensal and pathogenic Neisseria species.

BACKGROUND: Horizontal gene transfer is an important source of genetic variation among Neisseria species and has contributed to the spread of resistance to penicillin and sulfonamide drugs in the pathogen Neisseria meningitidis. Sulfonamide resistance in Neisseria meningitidis is mediated by altered chromosomal folP genes. At least some folP alleles conferring resistance have been horizontally acquired from other species, presumably from commensal Neisseriae. In this work, the DNA sequence surrounding folP in commensal Neisseria species was determined and compared to corresponding regions in pathogenic Neisseriae, in order to elucidate the potential for inter-species DNA transfer within this region. RESULTS: The upstream region of folP displayed differences in gene order between species, including an insertion of a complete Correia element in Neisseria lactamica and an inversion of a larger genomic segment in Neisseria sicca, Neisseria subflava and Neisseria mucosa. The latter species also had DNA uptake signal sequences (DUS) in this region that were one base different from the DUS in pathogenic Neisseriae. Another interesting finding was evidence of a horizontal transfer event from Neisseria lactamica or Neisseria cinerea that introduced a novel folP allele to the meningococcal population. CONCLUSION: Genetic recombination events immediately upstream of folP and horizontal transfer have resulted in sequence differences in the folP region between the Neisseria species. This variability could be a consequence of the selective pressure on this region exerted by the use of sulfonamide drugs.

Chromosomes, Bacterial↗

PubMed2003

The putative transcriptional activator MSN1 promotes chromium accumulation in Saccharomyces cerevisiae.

Yeast is a good system for studying molecular mechanisms of metal tolerance. Using a mini-Tn mutagenized yeast pool, we isolated a chromate-tolerant mutant, CrT9, that displayed metal-specific tolerance since it was only tolerant to Cr(VI), not to Cr(III), Cd, As, or Fe. The Cr-tolerance of CrT9 appeared to be due to reduced Cr accumulation as it accumulated only 56% as much as WT (Y800). Using IPCR (inverse PCR), we found that the mini-Tn had been inserted at nt 741 of the transcriptional activator, MSN1. MSN1 is a multifunctional protein involved in invertase activity, iron uptake, starch degradation, pseudohyphal growth, and osmotic gene expression. We found that there was only one mini-Tn insertion in CrT9 since MSN1 and mini-Tn probes hybridized to the same DNA fragment, and the MSN1 probe detected an enlarged MSN1 mRNA. When we over-expressed MSN1 in CrT9 and WT, both accumulated larger amounts of Cr. We conclude that Cr accumulation in S. cerevisiae is promoted by the transcriptional activator MSN1.

Chromium↗

PubMed1993

Differential usage of the carboxyl-terminal region among aldolase isozymes.

Sequence homology among nonconserved residues 357-362 of the COOH-terminal region in fructose-1,6-bisphosphate aldolases correlates with isozyme classification of aldolases. Recombinant chimers of human liver and maize aldolases were constructed by exchanging residues 357-362 with those from muscle, maize, and liver isozyme and by insertion in the maize sequence at position 349 rabbit muscle and liver residues 346-349. Activity variation among the chimers relative to native controls ranged from less than 10% to greater than 300% of Vm. Exchange of residues 357-362 significantly affected both Vm and Km without modifying catalytic efficiency kcat/Km, whereas insertion of residues 346-349 modified Vm and Km and increased catalytic efficiency. Steady state carbanion oxidation rates varied inversely with activity and were differentially affected with respect to equilibrium oxidation rates. Sequence exchange of residues 357-362 appears to modulate carbanion proton exchange, whereas sequence insertion of residues 346-349 modifies substrate and aldehyde interaction with C6 phosphate binding locus. Low intrinsic susceptibility to carboxypeptidase A degradation of the COOH terminus in liver aldolase is consistent with tight association of this COOH terminus in a conformation unfavorable for promoting high catalytic activity. Efficient carbanion protonation promoted by specific sequences 357-362 represents a mechanistic feature which distinguishes catalytically active maize and muscle isozymes from less active liver isozyme. Conservation of active site residues among aldolases suggests that isozyme diversity among aldolases arose from divergent evolution of the COOH-terminal sequence.

Amino Acid Sequence↗

PubMed2006

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms.

Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended "NT-AARA" motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes.

Alu Elements↗

PubMed2007

Microhomologies between T-DNA ends and target sites often occur in inverted orientation and may be responsible for the high frequency of T-DNA-associated inversions.

Sequence analysis of left and right border integration sites of independent, single-copy T-DNA inserts in Arabidopsis thaliana revealed three previously unrecognized concomitants of T-DNA integration. First, genomic pre-insertion sites shared sequence similarity not only with the T-DNA left and right border regions, as was previously reported, but also at high frequency with the inverted complement of the T-DNA right border region. Second, palindromic sequences were frequently found to overlap or lie adjacent to genomic target sites, suggesting a high recombinogenic potential for palindromic elements during T-DNA integration and a possible role during the primary contact between the T-DNA and the target DNA. Third, "filler" DNA sequences between genomic pre-insertion site DNA and T-DNA often derive from sequences in the T-DNA left and right border regions that are clustered around palindromic sequences in these T-DNA regions, suggesting that these palindromic elements are "hot spots" for filler DNA formation. The discovery of inverted sequence similarities at the right border suggests a previously unrecognized mode of T-DNA integration that involves heteroduplex formation at both T-DNA borders and with opposite strands of the target DNA. Scanning for sequence similarities in both direct and inverted orientation may increase the probability and/or effectiveness of anchoring the T-DNA to the target DNA. Variations on this scheme may also account for inversion events at the target site of T-DNA integration and inverted T-DNA repeat formation, common sequence organization patterns associated with T-DNA integration.

Arabidopsis↗

PubMed1996

Genetic dissection of sexual orientation: behavioral, cellular, and molecular approaches in Drosophila melanogaster.

Insertional mutagenesis using P-element vectors yielded several independent mutations that cause male homosexuality in Drosophila melanogaster. Subsequent analyses revealed that all of these insertions were located at the same chromosomal division, 91B, where one of the inversion breakpoints responsible for the bisexual phenotype of the fruitless (fru) mutant has been mapped. In addition to the altered sexual orientation, the fru mutants displayed a range of defects in the formation of a male-specific muscle, the muscle of Lawrence. Since the male-specific formation of this muscle was dependent solely on the sex of the innervating nerve and not on the sex of the muscle itself, the primary site of action of the fru gene should be in the neural cells. satori, one of the P-insertion alleles of fru which we isolated, carried the lacZ gene of E. coli as a reporter, and beta-galactosidase expression was found in a subset of brain cells including those in the antennal lobe in the satori mutant. Targeted expression of a sex determination gene, transformer (tra), was used to produce chromosomally male flies with certain feminized glomeruli in the antennal lobe. Such sexually mosaic flies courted not only females but also males when the DM2, DA3 and DA4 glomeruli were feminized, indicating that these substructures in the antennal lobe may be involved in the determination of the sexual orientation of flies. Molecular cloning and analyses of the genomic and complementary DNAs indicated that transcription of the fru locus yields several different transcripts, one of which encodes a putative transcription regulator with a BTB domain and two zinc finger motifs. In the 5' non-coding region, three putative Transformer binding sites were identified. It appears plausible therefore that the fru gene is one of the elements in the sex determination cascade that controls sexual fates of certain neuronal cells. Improper sex determination in these neural cells may lead to altered sexual orientation and malformation of the male-specific muscle. Some implications of the results of our study on sexual orientation in other organisms will be discussed based on the Drosophila research.

Amino Acid Sequence↗

PubMed2002

Homologous recombination between the inverted terminal repeats of defective transposon TCp3.2 causes an inversion in the genome of Cydia pomonella granulovirus.

In this study, a new mutant of the Cydia pomonella granulovirus (CpGV), which shows spontaneous inversion of a transposable element during in vivo replication, is described. CpGV-MCp4 is a natural mutant of CpGV-M, containing the transposable element TCp3.2, which originated from the genome of the host C. pomonella. During in vivo cloning studies of CpGV-MCp4, a mutant called CpGV-MCp4inv was isolated. CpGV-MCp4inv shows heterogeneity in the genome area of transposon insertion. Restriction mapping, PCR analysis and subsequent sequence analysis gave strong evidence that an inversion of TCp3.2 is caused by homologous recombination between the long inverted terminal repeats (ITRs) of the transposon. This finding demonstrated that extensive homologous repeat regions such as the ITRs of transposons cause inversions by homologous recombination during in vivo replication. The observed in vivo inversion between the ITRs can be considered as a model for the contribution of repeated sequences in the genome rearrangement of baculoviruses and a source for genetic heterogeneity among different baculoviruses and baculovirus genotypes.

Animals↗

PubMed2005

Identification of 32 novel mutations in the factor VIII gene in Indian patients with hemophilia A.

Seventy-five unrelated hemophilia A patients from India were analyzed for factor VIII gene defects. Intron 22 inversion was identified in 22 patients and intron 1 inversion in 2 patients. In the remaining 51 patients without inversions screening the FVIII gene by denaturing high performance liquid chromatography (DHPLC) revealed 42 different mutations in 44 unrelated subjects. These included 14 missense, 7 nonsense, 9 splice site, 8 deletional, 3 insertional mutations and one indel mutation. Of these, 32 were novel gene alterations. The hotspots included intron 22 inversion, CpG and adenine runs.

Binding Sites↗

PubMed2002

Structure and chromosomal distribution of human mitochondrial pseudogenes.

Nuclear mitochondrial pseudogenes (Numts) have been found in the genome of many eukaryote species, including humans. Using a BLAST approach, we found 1105 DNA sequences homologous to mitochondrial DNA (mtDNA) in the August 2001 Goldenpath human genome database. We assembled these sequences manually into 286 pseudogenes on the basis of single insertion events and constructed a chromosomal map of these Numts. Some pseudogenes appeared highly modified, containing inversions, deletions, duplications, and displaced sequences. In the case of four randomly selected Numts, we used PCR tests on cells lacking mtDNA to ensure that our technique was free from genome-sequencing artifacts. Furthermore, phylogenetic investigation suggested that one Numt, apparently inserted into the nuclear genome 25-30 million years ago, had been duplicated at least 10 times in various chromosomes during the course of evolution. Thus, these pseudogenes should be very useful in the study of ancient mtDNA and nuclear genome evolution.

Chromosome Mapping↗

PubMed1995

Screening for mutations in haemophilia A patients by multiplex PCR-SSCP, Southern blotting and RNA analysis: the detection of a genetic abnormality in the factor VIII gene in 30 out of 35 patients.

The molecular characterization of mutations in haemophilia A patients in this study was carried out by PCR-SSCP, Southern blotting, and reverse transcribed-PCR. A multiplex PCR in which four to eight exons were co-amplified was developed to reduce the time needed for screening the coding region of the factor VIII gene. PCR-SSCP was used to screen for small molecular defects, and reverse transcriptase PCR combined with Southern blotting was used to screen DNA for the inversions that occur frequently in intron 22 of the factor VIII gene. A group of 35 haemophilia A patients was analysed by these methods and 31 mutations were detected. In one patient two mutations were identified. The cases of mild and moderate haemophilia A showed changes in single nucleotides which predicted amino acid changes. The patients affected by severe haemophilia A showed two types of mutations. First, deletions or insertions that result in a frameshift in the coding DNA sequence were observed. Second, inversions were found which result in a disruption of the gene. With the screening strategies used we succeeded in elucidating an abnormality in the factor VIII gene in 30/35 haemophilia A patients.

Base Sequence↗

PubMed1989

I elements of Drosophila melanogaster generate specific chromosomal rearrangements during transposition.

We report a detailed molecular analysis of three chromosomal rearrangements, which have been produced during I-R hybrid dysgenesis in Drosophila melanogaster. They all disrupt the yellow gene. One of them is a deletion; the other two are inversions, which may be interpreted as the results of recombination events between I elements inserted at their break points. These events appear to occur at the time of transposition and involve integrating rather than resident I elements. They are produced by a mechanism very similar to homologous ectopic recombination.

Animals↗

PubMed1988

P element insertions and rearrangements at the singed locus of Drosophila melanogaster.

DNA from the singed gene of Drosophila melanogaster was isolated using an inversion between a previously cloned P element at cytological location 17C and the hypermutable allele singed-weak. Five out of nine singed mutants examined have alterations in their DNA maps in this region. The singed locus is a hotspot for mutation during P-M hybrid dysgenesis, and we have analyzed 22 mutations induced by P-M hybrid dysgenesis. All 22 have a P element inserted within a 700-bp region. The precise positions of 10 P element insertions were determined and they define 4 sites within a 100-bp interval. During P-M hybrid dysgenesis, the singed-weak allele is destabilized, producing two classes of phenotypically altered derivatives at high frequency. In singed-weak, two defective P elements are present in a "head-to-head" or inverse tandem arrangement. Excision of one element results in a more extreme singed bristle phenotype while excision of the other leads to a wild-type bristle phenotype.

Alleles↗