Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Allele replacement”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources
PubMed2002

Proprotein processing within secretory dense core granules of Tetrahymena thermophila.

In the ciliate Tetrahymena thermophila, the polypeptides stored in secretory dense core granules (DCGs) are generated by proteolytic processing of precursors, and the mature products assemble as a crystal. Previous observations suggested that this maturation involves precise cleavage at distinct motifs by a small number of enzymes. To test these inferences, we analyzed the determinants for site-specific processing of pro-Grl1p (Granule lattice protein 1) by complete gene replacement with modified alleles. Contrary to the predictions of previous models, none of the component amino acids in a putative processing motif was necessary for targeted cleavage. Indeed, cleavage at a range of alternative positions near the native site was consistent with normal DCG assembly. Furthermore, substitution of other classes of processing site motifs did not perturb DCG structure or function. These results suggest that processing can be catalyzed by multiple proteases, for which substrate accessibility may be the prime determinant of site specificity. Consistent with this, inhibition of either subtilisin or cathepsin family proteases resulted in delayed processing of pro-Grl1p.

Amino Acid Sequence↗
PubMed2001

Alanine-scanning mutagenesis of Aspergillus gamma-tubulin yields diverse and novel phenotypes.

We have created 41 clustered charged-to-alanine scanning mutations of the mipA, gamma-tubulin, gene of Aspergillus nidulans and have created strains carrying these mutations by two-step gene replacement and by a new procedure, heterokaryon gene replacement. Most mutant alleles confer a wild-type phenotype, but others are lethal or conditionally lethal. The conditionally lethal alleles exhibit a variety of phenotypes under restrictive conditions. Most have robust but highly abnormal mitotic spindles and some have abnormal cytoplasmic microtubule arrays. Two alleles appear to have reduced amounts of gamma-tubulin at the spindle pole bodies and nucleation of spindle microtubule assembly may be partially inhibited. One allele inhibits germ tube formation. The cold sensitivity of two alleles is strongly suppressed by the antimicrotubule agents benomyl and nocodazole and a third allele is essentially dependent on these compounds for growth. Together our data indicate that gamma-tubulin probably carries out functions essential to mitosis and organization of cytoplasmic microtubules in addition to its well-documented role in microtubule nucleation. We have also placed our mutations on a model of the structure of gamma-tubulin and these data give a good initial indication of the functionally important regions of the molecule.

Alanine↗
PubMed1994

The SUP35 omnipotent suppressor gene is involved in the maintenance of the non-Mendelian determinant [psi+] in the yeast Saccharomyces cerevisiae.

The SUP35 gene of yeast Saccharomyces cerevisiae encodes a 76.5-kD ribosome-associated protein (Sup35p), the C-terminal part of which exhibits a high degree of similarity to EF-1 alpha elongation factor, while its N-terminal region is unique. Mutations in or overexpression of the SUP35 gene can generate an omnipotent suppressor effect. In the present study the SUP35 wild-type gene was replaced with deletion alleles generated in vitro that encode Sup35p lacking all or a part of the unique N-terminal region. These 5'-deletion alleles lead, in a haploid strain, simultaneously to an antisuppressor effect and to loss of the non-Mendelian determinant [psi+]. The antisuppressor effect is dominant while the elimination of the [psi+] determinant is a recessive trait. A set of the plasmid-borne deletion alleles of the SUP35 gene was tested for the ability to maintain [psi+]. It was shown that the first 114 amino acids of Sup35p are sufficient to maintain the [psi+] determinant. We propose that the Sup35p serves as a trans-acting factor required for the maintenance of [psi+].

Amino Acid Sequence↗
PubMed2004

Pax3:Fkhr interferes with embryonic Pax3 and Pax7 function: implications for alveolar rhabdomyosarcoma cell of origin.

To investigate the role of the translocation-associated gene Pax3:Fkhr in alveolar rhabdomyosarcomas, we generated a Cre-mediated conditional knock-in of Pax3:Fkhr into the mouse Pax3 locus. Exploring embryonic tumor cell origins, we replaced a Pax3 allele with Pax3:Fkhr throughout its expression domain, causing dominant-negative effects on Pax3 and paradoxical activation of the Pax3 target gene, c-Met. Ectopic neuroprogenitor cell proliferation also occurs. In contrast, activation later in embryogenesis in cells that express Pax7 results in viable animals with a postnatal growth defect and a moderately decreased Pax7+ muscle satellite cell pool, phenocopying Pax7 deficiency but remarkably not leading to tumors.

Animals↗
PubMed1994

Targeted mutagenesis of the phospholipase D gene results in decreased virulence of Corynebacterium pseudotuberculosis.

The chromosomal gene encoding the phospholipase D from Corynebacterium pseudotuberculosis (biovar ovis) isolate Whetten 1 was replaced with an allele containing a nonsense mutation. The virulence of the mutant strain (W1.31r1) and the isogenic parental strain were then compared by inoculation of goats. The wild-type strain caused abscessation at the site of infection, which then spread to the regional lymph node, while W1.31r1 had a reduced ability to establish a primary infection and was incapable of dissemination. Our results confirm that phospholipase D is a virulence determinant of C. pseudotuberculosis that increases the persistence and spread of the bacteria within the host.

Amino Acid Sequence↗
PubMed1989

Cloning and characterization of the Haemophilus influenzae Rd rec-1+ gene.

The Haemophilus influenzae Rd rec-1+ gene was cloned from a partial chromosomal digest into a plasmid vector as a 20-kilobase-pair (kbp) BstEII fragment and then subcloned. The smallest subclone with rec-1+ activity carried a 3.1-kbp EcoRI fragment. The identity of the rec-I gene in these clones was confirmed by transforming an Rd strain carrying a leaky rec-1 mutation (recA4) to resistance to methyl methanesulfonate (MMS) by using whole or digested plasmids. It was demonstrated that the Rec+ phenotype of the MMSr transformants was linked to the strA, novAB, and mmsA loci, as expected if the recA4 allele had been replaced by rec-1+. In growing cultures (rec-1 or rec+), all rec-1+-carrying plasmids induced near-maximal levels of transformability when their hosts reached stationary phase; these levels are 100 to 1,000 times higher than the values seen with strains not carrying a Rec plasmid. Transfer of the 3.1-kbp subclone was greatly reduced compared with transfer of similarly sized vector plasmids, and the resulting transformants grew slowly; this suggests an explanation of my failure to directly clone this fragment from chromosomal DNA digests. Transfer of a rec-1+ plasmid to a very poorly genetically transformable H. influenzae Rb strain resulted in greatly increased transformability. Transfer of such plasmids to a noncompetent H. influenzae Rc strain did not render this strain competent. It is suggested that transformability of Rd and Rb strains is limited by rec-1 expression but that the noncompetence of Rc has some other basis.

Aerobiosis↗
PubMed1995

Nucleotide sequence, mutational analysis, transcriptional start site, and product analysis of nov, the gene which affects Escherichia coli K-12 resistance to the gyrase inhibitor novobiocin.

In a previous study, we demonstrated the existence of a gene locus, nov, which affects resistance of Escherichia coli K-12 to the gyrase inhibitor novobiocin and, to a lesser degree, coumermycin (J. Rakonjac, M. Milic, D. Ajdic, D. Santos, R. Ivanisevic, and D. J. Savic, Mol. Microbiol. 6:1547-1553, 1992). In the present study, sequencing of the nov gene locus revealed one open reading frame that encodes a protein of 54,574 Da, a value. found to be in correspondence with the size of the Nov protein identified in an in vitro translation system. We also located the 5' end of the nov transcript 8 bp downstream from a classical sigma70 promoter. Transcription of the gene is in the counterclockwise direction on the E. coli chromosome. Transposon mutagenesis of nov followed by complementation analyses and replacement of chromosomal alleles with mutated nov confirmed our previous assumption that the nov gene exists in two allelic forms and that the Novr gene is an active allele while the Novs gene is an inactive form. After comparing nucleotide sequences flanking the nov gene with existing data, we conclude that the gene order in this region of the E. coli K-12 map is att phi 80-open reading frame of unknown function-kch (potassium channel protein)-nov-opp. Finally, the possible identity of the nov gene with cls, the gene that codes for cardiolipin synthase, is also discussed.

Alleles↗
PubMed2001

Mutations in genes involved in the flagellar export apparatus of the solvent-tolerant Pseudomonas putida DOT-T1E strain impair motility and lead to hypersensitivity to toluene shocks.

Pseudomonas putida DOT-T1E is a solvent-tolerant strain able to grow in the presence of 1% (vol/vol) toluene in the culture medium. Random mutagenesis with mini-Tn5-'phoA-Km allowed us to isolate a mutant strain (DOT-T1E-42) that formed blue colonies on Luria-Bertani medium supplemented with 5-bromo-4-chloro-3-indolylphosphate and that, in contrast to the wild-type strain, was unable to tolerate toluene shocks (0.3%, vol/vol). The mutant strain exhibited patterns of tolerance or sensitivity to a number of antibiotics, detergents, and chelating agents similar to those of the wild-type strain. The mutation in this strain therefore seemed to specifically affect toluene tolerance. Cloning and sequencing of the mutation revealed that the mini-Tn5-'phoA-Km was inserted within the fliP gene, which is part of the fliLMNOPQRflhBA cluster, a set of genes that encode flagellar structure components. FliP is involved in the export of flagellar proteins, and in fact, the P. putida fliP mutant was nonmotile. The finding that, after replacing the mutant allele with the wild-type one, the strain recovered the wild-type pattern of toluene tolerance and motility unequivocally assigned FliP a function in solvent resistance. An flhB knockout mutant, another gene component of the flagellar export apparatus, was also nonmotile and hypersensitive to toluene. In contrast, a nonpolar mutation at the fliL gene, which encodes a cytoplasmic membrane protein associated with the flagellar basal body, yielded a nonmotile yet toluene-resistant strain. The results are discussed regarding a possible role of the flagellar export apparatus in the transport of one or more proteins necessary for toluene tolerance in P. putida DOT-T1E to the periplasm.

Alkaline Phosphatase↗
PubMed2001

uvrA is an acid-inducible gene involved in the adaptive response to low pH in Streptococcus mutans.

The pH-inducible acid tolerance response (ATR) is believed to play a major role in acid adaptation and virulence of Streptococcus mutans. To study this phenomenon in S. mutans JH1005, differential display PCR was used to identify and clone 13 cDNA products that had increased expression in response to pH 5.0 compared to that of pH 7.5-grown cells. One of these products, confirmed to be pH inducible by RNA dot blot and reverse transcription-PCR analyses, had 67% identity to a uvrA-UV repair excinuclease gene in Bacillus subtilis. Further sequence analysis of the uvrA homologue using the S. mutans genome database revealed that the complete gene was encoded in an open reading frame (ORF) of 2,829 bp (944 amino acids; 104.67 kDa). Immediately 3' of uvrA was an ORF encoding a putative aminopeptidase gene (pepP). uvrA knockouts were constructed in S. mutans strains JH1005, NG8, and UA159 using allelic-exchange mutagenesis, replacing the entire gene with an erythromycin resistance cassette. As with uvrA mutants in other bacteria, the S. mutans uvrA mutants were extremely sensitive to UV irradiation. The uvrA mutant of S. mutans JH1005 was also more sensitive than the wild type to growth at pH 5.0, showing a 15% reduction in growth rate and a 14% reduction in final resting culture density. Acid-adapted S. mutans JH1005 uvrA mutants were shown to be more resistant to UV irradiation than was the parent but were unable to survive exposure to a killing pH of 3.0. Moreover, agarose gel electrophoretic analysis of chromosomal DNA isolated from uvrA-deficient cells exposed to low pH demonstrated more DNA damage than that for the wild-type strain. Here we suggest that uvrA and the nucleotide excision repair pathway are involved in the repair of acid-induced DNA damage and are associated with successful adaptation of S. mutans to low pH.

Acids↗
PubMed1986

Mitotic gene conversion lengths, coconversion patterns, and the incidence of reciprocal recombination in a Saccharomyces cerevisiae plasmid system.

Plasmids capable of undergoing genetic exchange in mitotically dividing Saccharomyces cerevisiae cells were used to measure the length of gene conversion events, to determine patterns of coconversion when multiple markers were present, and to correlate the incidence of reciprocal recombination with the length of conversion tracts. To construct such plasmids, restriction site linkers were inserted both within the HIS3 gene and in the flanking sequences, and two different his3- alleles were placed in a vector. Characterization of the genetic exchanges in these plasmids showed that most occur with the conversion of one his3- allele. Many of these events included coconversions in which more than one marker along the allelic sequence was replaced. The frequency of coconversion decreased with the distance between two markers such that markers further than 1 kilobase apart were infrequently coconverted. From these results the average length of conversion was determined to be approximately 0.5 kilobase. Examination of coconversions involving three or more markers revealed an almost obligatory, simultaneous coconversion pattern of all markers. Thus, when two markers which flank an intervening marker are converted, the intervening marker is 20 times more likely to be converted than to remain unchanged. The results of these studies also showed that the incidence of reciprocal recombination, which accompanies more than 20% of the conversion events, is more frequent when the conversion tract is longer than average.

Crossing Over, Genetic↗
PubMed1988

Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable sextuple mutant.

Saccharomyces cerevisiae contains at least 24 distinct small nuclear RNAs (snRNAs), several of which are known to be essential for viability and to participate in the splicing of pre-mRNAs; the RNAs in this subset contain binding sites for the Sm antigen, a hallmark of metazoan snRNAs involved in mRNA processing. In contrast, we showed previously that the single-copy genes for three other snRNAs (snR3, snR4, and snR10) are not required for viability, although cells lacking snR10 are growth impaired at low temperature. None of these RNAs associates with the Sm antigen. To assess this apparent correlation, we cloned and sequenced the genes encoding three additional non-Sm snRNAs. Comparison of these genes with nine additional yeast snRNA genes revealed a highly conserved TATA box located 92 +/- 8 nucleotides 5' of the transcriptional start site. By using the technique of gene replacement with null alleles, each of these three single copy genes was shown to be completely dispensable. We constructed multiple mutants to test the hypothesis that, individually, each of these snRNAs is nonessential because the snRNAs play functionally overlapping roles. A mutant lacking five snRNAs (snR3, snR4, snR5, snR8, snR9) was indistinguishable from the wild type, and growth of the sextuple mutant was no more impaired than that in strains lacking only snR10. This widespread dispensability of snRNAs was completely unexpected and forces us to reconsider the possible roles of these ubiquitous RNAs.

Base Sequence↗
PubMed1998

Mating-type gene switching in Saccharomyces cerevisiae.

Saccharomyces cerevisiae can change its mating type as often as every generation by a highly choreographed, site-specific recombination event that replaces one MAT allele with different DNA sequences encoding the opposite allele. The study of this process has yielded important insights into the control of cell lineage, the silencing of gene expression, and the formation of heterochromatin, as well as the molecular events of double-strand break-induced recombination. In addition, MAT switching provides a remarkable example of a small locus control region--the Recombination Enhancer--that controls recombination along an entire chromosome arm.

Animals↗
PubMed1989

Genetic control of diabetogenesis in NOD/Lt mice. Development and analysis of congenic stocks.

Genetic outcross and backcross analysis of nonobese diabetic (NOD/Lt) mice with a related but diabetes-resistant strain, nonobese normal (NON/Lt), has demonstrated that susceptibility to insulin-dependent diabetes mellitus is controlled in a recessive fashion by multiple genetic loci, including one (Idd-1s) associated with H-2 on chromosome 17 and another (Idd-2s) associated with Thy-1b/Apoa-1b (formerly Alp-1) on chromosome 9. To analyze the separate pathogenic contributions of Idd-1s and Idd-2s, two distinct congenic stocks of NOD/Lt mice homozygous on chromosomes 17 and 9 for NON/Lt linkage markers for the respective resistance alleles (Idd-1r and Idd-2r) were developed. The recessive nature of Idd-1s was confirmed at the fifth backcross generation in that 83% of females and 29% of males homozygous for NOD H-2 haplotype developed diabetes, whereas no diabetes occurred in any of the mice homozygous or heterozygous for the NON haplotype. However, codominant and recessive MHC-associated susceptibility genes in this congenic stock were indicated by the finding that at least one copy of the NOD/Lt MHC was required for insulitis development. Virtually no insulitis was detected in the pancreases of mice homozygous for NON haplotype at 42 wk of age, whereas heavy generalized insulitis was present in 3 of 19 H-2 heterozygotes and in 7 of 7 diabetic and 3 of 5 nondiabetic mice homozygous for NOD haplotype. Further indication of the presence of MHC-associated codominant and recessive MHC-associated susceptibility genes was the observation that the NOD MHC haplotype correlated in a codominant fashion with a relative increase in the percentage of splenic T-lymphocytes bearing the Ly-2 surface marker. Severe insulitis and concomitant high diabetes incidences occurred in all genotypic classes of congenic mice carrying Thy-1/Apoa-1 linkage markers for either NOD or NON alleles at Idd-2. Molecular analysis indicated that the NON-derived Idd-2r resistance allele had been replaced by recombination with Idd-2s from NOD. Restriction-fragment-length polymorphism analysis of two polymorphic markers proximal to Thy-1, low-density lipoprotein receptor Ldlr and Ets-1, a protooncogene, confirmed a recombinant chromosome 9, because homozygosity for NOD genomic fragments was found centromeric to an NON congenic segment of at least 20 centiMorgans spanning the Thy-1 and Mod-1 loci.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2005

Generation of genetically-altered mice producing very low levels of coagulation factorVII.

It has been shown earlier that mice with a total targeted deletion of the factorVII gene (FVII(-/-)) die perinatally, thereby precluding study of adult animals with this total deficiency. Consequently, mice producing very low levels of FVII were developed by targeted replacement of the wild-type (WT) murine FYII gene with its corresponding cDNA, under control of the tetracycline transactivator (tTA) promoter. When backcrossed into the C57BI/6 strain, unchallenged mice containing two replaced FVII(tTA) alleles (FVII(tTA/tTA) produce approximately 0.7% of WT FVII levels, but yet live to adulthood despite displaying severely downregulated overall thrombin production and spontaneously developing cardiac fibrosis at a young adult age. This genetically-altered mouse line provides an excellent animal model to study consequences of a severe FVII deficiency in unchallenged mice and in mice subjected to a variety of experimental challenges.

Animals↗
PubMed1993

The M-N--V-A-B-D blood group system of chimpanzee and other apes: serology and genetics.

Poly- and monoclonal anti-M and anti-N reagents detect on the red cells of anthropoid apes the M and/or N antigens which are similar to, but not identical with human M and N. A series of V-A-B-D specificities, closely related to the M-N system, are recognized on ape red blood cells by chimpanzee immune sera. To account for the distributions of the M-N--V-A-B-D types in man and in various apes, a genetic model is proposed that assumes the existence of two independent pairs of alleles: M/m, and N/n. In the processes of speciation, some of the alleles were lost or replaced by multiple mutations, resulting in chimpanzee in a series of codominant alleles responsible for as many as 16 M-N--V-A-B-D phenotypes.

Alleles↗
PubMed1997

Alien introgression in rice.

Rice (Oryza sativa L.) productivity is affected by several biotic and abiotic stresses. The genetic variability for some of these stresses is limited in the cultivated rice germplasm. Moreover, changes in insect biotypes and disease races are a continuing threat to increased rice production. There is thus an urgent need to broaden the rice gene pool by introgressing genes for such traits from diverse sources. The wild species of Oryza representing AA, BB, CC, BBCC, CCDD, EE, FF, GG and HHJJ genomes are an important reservoir of useful genes. However, low crossability and limited recombination between chromosomes of cultivated and wild species limit the transfer of such genes. AT IRRI, a series of hybrids and monosomic alien addition lines have been produced through embryo rescue following hybridization between rice and several distantly related species. Cytoplasmic male sterility and genes for resistance to grassy stunt virus and bacterial blight have been transferred from A genome wild species into rice. Similarly, genes for resistance to brown planthopper, bacterial blight and blast have also been introgressed across crossability barriers from distanly related species into rice. Some of the introgressed genes have been mapped via linkage to molecular markers. One of the genes Xa-21 introgressed from O. longistaminata has been cloned and physically mapped on chromosome 11 of rice using BAC library and flourescence in-situ hybridization. RFLP analysis revealed introgression from 11 of the 12 chromosomes of C genome species into rice. Introgression has also been obtained from other distant genomes (EE, FF, GG) into rice and in majority of the cases one or two RFLP markers were introgressed. Reciprocal replacement of RFLP alleles of wild species with the alleles of O. sativa indicates alien gene transfer through crossing over. The rapid recovery of recurrent phenotypes in BC2 and BC3 generations from wide crosses is an indication of limited recombination. Further cytogenetic and molecular investigations are required to determine precisely the mechanism of introgression of small chromosome segments from distant genomes in the face of limited homoeologous chromosome pairing. Future research should focus on enhancing recombination between homoeologous chromosomes. Introgression of QTL from wild species should be attempted to increase the yield potential of rice.

Animals↗
PubMed2004

Genetic approaches to studying mouse models of human seizure disorders.

In conclusion, we have discussed a reverse genetics approach to studying seizure disorders in mice (Fig. 1), employing a targeted mutagenesis method to exploit the genetic defects identified in human epilepsy families. After detailed characterization of the nature of the human mutation and the mouse counterpart gene, a targeting vector containing the human disease allele is created. The endogenous mouse gene is replaced by the human disease allele through homologous recombination in ES cells, leading to the generation of chimeric animals. Mice carrying one copy or both copies of the human mutation can be bred to study the phenotypic effect of heterozygous and homozygous mutations. At this stage, one may want to split the newly created mice into two groups. One group will go through seizure phenotyping tests, while the other group will be used to generate disease allele-carrying mice on a different genetic background. Phenotypic characterization of mice on different inbred strains includes behavioral monitoring and EEG analysis looking for the occurrence of spontaneous seizures, as well as routine cage examination looking for handling-provoked seizure and ECT- and PTZ- induced seizure paradigms looking for sensitivity to these stimuli. A complete evaluation of the seizure phenotype at the whole-animal level establishes the relevance of the mouse model to the human condition. Further investigation including imaging, electrophysiology and AED response in these mouse models will shed light on the mechanistic basis of the convulsive disorder. Current epilepsy research in mouse genetics offers promise for understanding the molecular mechanisms that underlie epileptogenesis in humans. A large-scale forward genetic effort to create novel mouse mutants with seizure phenotypes by in vivo chemical mutagenesis with ethyl-nitroso urea (ENU) is underway at the Jackson Laboratory (http://www.jax.org/nmf/). Genetic mapping and isolation of the affected genes in these seizure-prone models will provide additional molecular pathways involved in seizures. The mutant mice generated through both forward and reverse genetic approaches will be a valuable resource for the biomedical community to study epilepsy at the molecular level and to characterize the pathological consequences of seizures in the whole organism.

Animals↗
PubMed1993

Construction of chimeric alleles with altered specificity at the b incompatibility locus of Ustilago maydis.

Multiallelic incompatibility systems found in many fungi and plants function to limit inbreeding by mediating self versus nonself recognition. The plant pathogenic fungus Ustilago maydis has a locus called b that governs incompatibility. Two multiallelic genes, bE and bW, are present at the b locus. Fusion of haploid strains carrying different alleles at bE and bW establishes an infectious dikaryon capable of pathogenesis on maize (Zea mays). Cells carrying a single type of b locus, whether haploid or dikaryotic, are nonpathogenic. To identify sequences within the bE gene that determine allelic specificity, targeted gene replacement was employed to produce a series of chimeras between the b1E and b2E alleles. Incompatibility tests with strains carrying the chimeric alleles identified a 30- to 48-amino acid region responsible for specificity. Suprisingly, the chimeras with recombination points within this region had a specificity different from both parent alleles. Overall, these results define an important domain in bE involved in self versus nonself recognition.

Alleles↗