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Results for “mutagenesis screen”

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PubMed2003

Dissecting the EphA3/Ephrin-A5 interactions using a novel functional mutagenesis screen.

The EphA3 receptor tyrosine kinase preferentially binds ephrin-A5, a member of the corresponding subfamily of membrane-associated ligands. Their interaction regulates critical cell communication functions in normal development and may play a role in neoplasia. Here we describe a random mutagenesis approach, which we employed to study the molecular determinants of the EphA3/ephrin-A5 recognition. Selection and functional characterization of EphA3 point mutants with impaired ephrin-A5 binding from a yeast expression library defined three EphA3 surface areas that are essential for the EphA3/ephrin-A5 interaction. Two of these map to regions identified previously in the crystal structure of the homologous EphB2-ephrin-B2 complex as potential ligand/receptor interfaces. In addition, we identify a third EphA3/ephrin-A5 interface that falls outside the structurally characterized interaction domains. Functional analysis of EphA3 mutants reveals that all three Eph/ephrin contact areas are essential for the assembly of signaling-competent, oligomeric receptor-ligand complexes.

Binding Sites↗
PubMed1993

Evidence of mobilization of hobo transposons in a P-element mutagenesis screen.

In Drosophila melanogaster, mutations in Su(var) and En(var) loci either suppress or enhance position effect variegation, respectively. Towards the cloning of these genes we have induced, recovered, and characterized a series of Su(var) mutations located on the third chromosome. These mutations were recovered from a P-element mutagenesis scheme in which the third chromosome P[ry+ delta 2-3](99B) element would provide transposase in trans to mobilize a single nonautonomous P transposon, P[pUCHSNeo](9C), located on the X chromosome. Although this cross scheme induces mobilization of the X-chromosome P transposons and its subsequent reinsertion onto the autosomes, none of the Su(var) mutations recovered could be associated with P-transposon insertions. Further investigation of these mutations by in situ hybridization showed that another mobile element that can be mobilized in hybrids, hobo, was associated with these mutations. We conclude that the mobilization and reinsertion of the hobo elements, through an inadvertent hybrid HE dysgenic cross, is most likely responsible for the Su(var) mutations recovered from this P-element mutagenesis. The association of hobo element with this Su(var) locus will facilitate its cloning and offers the possibility of hobo transposon tagging other Su(var) loci.

Animals↗
PubMed2025

A base editor facilitates simultaneous purine and pyrimidine substitutions for ex vivo and in vivo mutagenesis screens.

Genetic mutations are closely linked to human diseases, yet the relationship between many mutations and their corresponding phenotypes remains poorly understood. Furthermore, tools to study the connection between nucleotide variations and phenotypes are limited. To address this issue, we developed ACGBEmax by fusing the dual-functional deaminase, engineered N-methylpurine DNA glycosylase, and evolved SOS response associated peptidase domain with nCas9(D10A). ACGBEmax enables the precise conversion of A, C, and G to other bases in mammalian cells, thereby generating an extensive range of base mutations types. We used ACGBEmax to generate HPRT variants, identifying mutations conferring resistance to 6-thioguanine. Additionally, we performed in situ mutagenesis of Ctnnb1 in mouse liver, identifying both known and potential oncogenic mutations. Our results prove that ACGBEmax is a powerful tool for generating a wide spectrum of mutation types at specific gene loci, highlighting its significant potential for applications in functional screening and the directed evolution of protein variants.

Animals↗
PubMed1999

Large numbers of mice established by in vitro fertilization with cryopreserved spermatozoa: implications and applications for genetic resource banks, mutagenesis screens, and mouse backcrosses.

Recent advances in the methodologies for cryopreservation of mouse spermatozoa have opened up a number of opportunities for mouse geneticists. We have investigated various applications for this relatively new technology and have explored the potential of sperm freezing coupled with IVF for archiving, stock building, and the rapid establishment of backcrosses. Firstly, we investigated the use of sperm freezing for the archiving of (C3H/HeH x BALB/c)F(1) progeny from a large-scale mutagenesis program. We have demonstrated that it is possible to establish efficient, comprehensive, and deep archives and that potentially thousands of offspring can be derived from the frozen spermatozoa of a single mutant male mouse. Secondly, we examined the efficacy of sperm freezing for a number of other genotypes. For at least some genotypes, frozen spermatozoa can be utilized to rapidly build stock far more quickly than by conventional methods. Finally, we demonstrated that it is feasible to use frozen spermatozoa from the mouse mutant archive for the rapid generation of mutant backcross progeny.

Animals↗
PubMed2006

The use of genomewide ENU mutagenesis screens to unravel complex mammalian traits: identifying genes that regulate organ-specific and systemic autoimmunity.

T-cell development is perhaps one of the best understood processes of mammalian cell differentiation, as many of the genes and pathways have been identified. By contrast, relatively little is known about the genes and pathways involved in immunological tolerance to self-antigens. Here, we describe the challenges associated with a genomewide screen designed at identifying new immune regulatory genes that uses a model of organ-specific autoimmunity leading to type 1 diabetes. The successful propagation and identification of the new gene variants will shed light on the various developmental checkpoints in lymphocyte development that are crucial for establishing tolerance to self-antigens.

Animals↗
PubMed2005

Using genomewide mutagenesis screens to identify the genes required for neural tube closure in the mouse.

BACKGROUND: Neural tube closure is a critical embryological process that requires the coordination of many molecular and cellular events. Only recently has the molecular basis of the cell movements that drive neural tube closure begun to be elucidated. This has been accomplished in part due to the analysis of a growing number of genetically targeted and naturally occurring mouse mutant strains that have neural tube defects (NTDs). Currently there are more than 100 genes that when mutated result in NTDs in the mouse. Yet only approximately 10% of genes in the mouse genome have been mutated and their gross phenotype analyzed, suggesting that only a small percentage of the genes that can cause NTDs have been identified. METHODS: In order to more systematically and fully understand the genetic basis of neural tube closure and to begin to define the molecular pathways that direct this key embryonic event, our laboratories have undertaken a forward genetic screen in mice. From this we hope to gain a better understanding of the regulation of this complex morphogenic processes. CONCLUSIONS: The mouse provides a good model for human neural tube closure, and therefore the information gained from generating novel mouse models of NTDs will help to predict the genes responsible for human NTDs and provide experimental evidence for how they function.

Animals↗
PubMed2006

[Mutagenesis, screening and characterization of mutants known as peroxisome biogenesis disorders in yeast].

Peroxisomes are essential for organisms' development and physiology. This fact is underscored by the lethality of a group of genetic disorders collectively known as the peroxisome biogenesis disorders (PBDs), such as Zellweger syndrome, in which peroxisomes fail to assemble properly. Defining the molecular bases of the PBDs has been the impetus behind the identification of the genes controlling peroxisome assembly, the PEX genes, from various modern organisms. Here as a original strain, Yarrowia lipolytica E122 was mutated by diethyl sulfate (DES) treatment and two mutants including temperature sensitive one were obtained. Compared to the initial strain, the two mutants showed more diffuse pattern of fluorescence characteristic of a cytosolic localization in immunofluorescence analysis, and showed no morphologically recognizable peroxisomes in electron micrographs. The two mutants arose from new gene mutation characterized by transformation and will be very useful in identification of new gene controlling peroxisome assembly from yeast.

Cytosol↗
PubMed2006

High-throughput random mutagenesis screen reveals TRPM8 residues specifically required for activation by menthol.

Menthol is a cooling compound derived from mint leaves and is extensively used as a flavoring chemical. Menthol activates transient receptor potential melastatin 8 (TRPM8), an ion channel also activated by cold, voltage and phosphatidylinositol-4,5-bisphosphate (PIP2). Here we investigated the mechanism by which menthol activates mouse TRPM8. Using a new high-throughput approach, we screened a random mutant library consisting of approximately 14,000 individual TRPM8 mutants for clones that are affected in their response to menthol while retaining channel function. We identified determinants of menthol sensitivity in two regions: putative transmembrane segment 2 (S2) and the C-terminal TRP domain. Analysis of these mutants indicated that activation by menthol involves a gating mechanism distinct and separable from gating by cold, voltage or PIP2. Notably, TRP domain mutations mainly attenuated menthol efficacy, suggesting that this domain influences events downstream of initial binding. In contrast, S2 mutations strongly shifted the concentration dependence of menthol activation, raising the possibility that S2 influences menthol binding.

Amino Acid Sequence↗
PubMed1992

Random PCR mutagenesis screening of secreted proteins by direct expression in mammalian cells.

We have developed a general method for screening randomly mutagenized expression libraries in mammalian cells by using fluorescence-activated cell sorting (FACS). The cDNA sequence of a secreted protein is randomly mutagenized by PCR under conditions of reduced Taq polymerase fidelity. The mutated DNA is inserted into an expression vector encoding the membrane glycophospholipid anchor sequence of decay-accelerating factor (DAF) fused to the C terminus of the secreted protein. This results in expression of the protein on the cell surface in transiently transfected mammalian cells, which can then be screened by FACS. This method was used to isolate mutants in the kringle 1 (K1) domain of tissue plasminogen activator (t-PA) that would no longer be recognized by a specific monoclonal antibody (mAb387) that inhibits binding of t-PA to its clearance receptor. DNA sequence analysis of the mutants and localization of the mutated residues on a three-dimensional model of the K1 domain identified three key discontinuous amino acid residues that are essential for mAb387 binding. Mutants with changes in any of these three residues were found to have reduced binding to the t-PA receptor on human hepatoma HepG2 cells but to retain full clot lysis activity.

Amino Acid Sequence↗
PubMed2003

Identification of Jade1, a gene encoding a PHD zinc finger protein, in a gene trap mutagenesis screen for genes involved in anteroposterior axis development.

In a gene trap screen for genes expressed in the primitive streak and tail bud during mouse embryogenesis, we isolated a mutation in Jade1, a gene encoding a PHD zinc finger protein previously shown to interact with the tumor suppressor pVHL. Expressed sequence tag analysis indicates that Jade1 is subject to posttranscriptional regulation, resulting in multiple transcripts and at least two protein isoforms. The fusion Jade1-beta-galactosidase reporter produced by the gene trap allele exhibits a regulated expression during embryogenesis and localizes to the nucleus and/or cytoplasm of different cell types. In addition to the primitive streak and tail bud, beta-galactosidase activity was found in other embryonic regions where pluripotent or tissue-specific progenitors are known to reside, including the early gastrulation epiblast and the ventricular zone of the cerebral cortex. Prominent reporter expression was also seen in the extraembryonic tissues as well as other differentiated cell types in the embryo, in particular the developing musculature. We show that the gene trap mutation produces a null allele. However, homozygotes for the gene trap integration are viable and fertile. Database searches identified a family of Jade proteins conserved through vertebrates. This raises the possibility that the absence of phenotype is due to a functional compensation by other family members.

Amino Acid Sequence↗
PubMed1998

Alanine screening mutagenesis establishes tyrosine 60 of bovine insulin-like growth factor binding protein-2 as a determinant of insulin-like growth factor binding.

The determinants of insulin-like growth factor (IGF) binding to its binding proteins (IGFBPs) are poorly characterized in terms of important residues in the IGFBP molecule. We have previously used tyrosine iodination to implicate Tyr-60 in the IGF-binding site of bovine IGFBP-2 (Hobba, G. D., Forbes, B. E., Parkinson, E. J., Francis, G. L., and Wallace, J. C. (1996) J. Biol. Chem. 271, 30529-30536). In this report, we show that the mutagenic replacement of Tyr-60 with either Ala or Phe reduced the affinity of bIGFBP-2 for IGF-I (4.0- and 8.4-fold, respectively) and for IGF-II (3.5- and 4.0-fold, respectively). Although adjacent residues Val-59, Thr-61, Pro-62, and Arg-63 are well conserved in IGFBP family members, Ala substitution for these residues did not reduce the IGF affinity of bIGFBP-2. Kinetic analysis of the bIGFBP-2 mutants on IGF biosensor chips in the BIAcore instrument revealed that Tyr-60 --> Phe bIGFBP-2 bound to the IGF-I surface 3.0-fold more slowly than bIGFBP-2 and was released 2.6-fold more rapidly than bIGFBP-2. We therefore propose that the hydroxyl group of Tyr-60 participates in a hydrogen bond that is important for the initial complex formation with IGF-I and the stabilization of this complex. In contrast, Tyr-60 --> Ala bIGFBP-2 associated with the IGF-I surface 5.0-fold more rapidly than bIGFBP-2 but exhibited an 18.4-fold more rapid release from this surface compared with bIGFBP-2. Thus both the aromatic nature and the hydrogen bonding potential of the tyrosyl side chain of Tyr-60 are important structural determinants of the IGF-binding site of bIGFBP-2.

Animals↗
PubMed2006

Comparison of imatinib mesylate, dasatinib (BMS-354825), and nilotinib (AMN107) in an N-ethyl-N-nitrosourea (ENU)-based mutagenesis screen: high efficacy of drug combinations.

BMS-354825 (dasatinib) and AMN107 (nilotinib) are potent alternate Abl inhibitors with activity against many imatinib mesylate-resistant BCR-ABL kinase domain (KD) mutants, except T315I. We used N-ethyl-N-nitrosourea (ENU)-exposed Ba/F3-p210(BCR-ABL) cells to compare incidence and types of KD mutants emerging in the presence of imatinib mesylate, dasatinib, and nilotinib, alone and in dual combinations. Although ENU is expected to induce mutations in multiple proteins, resistant clones were almost exclusively BCR-ABL KD mutant at relevant concentrations of nilotinib and dasatinib, consistent with a central role of KD mutations for resistance to these drugs. Twenty different mutations were identified with imatinib mesylate, 10 with nilotinib (including only 1 novel mutation, E292V) and 9 with dasatinib. At intermediate drug levels the spectrum narrowed to F317V and T315I for dasatinib and Y253H, E255V, and T315I for nilotinib. Thus, cross-resistance is limited to T315I, which is also the only mutant isolated at drug concentrations equivalent to maximal achievable plasma trough levels. With drug combinations maximal suppression of resistant clone outgrowth was achieved at lower concentrations compared with single agents, suggesting that such combinations may be equipotent to higher-dose single agents. However, sequencing uniformly revealed T315I, consistent with the need for a T315I inhibitor, to completely block resistance.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2005

Screening of flocculant-producing strains by NTG mutagenesis.

Screening of new microorganism being able to produce efficiently flocculants was carried out. A new model for screening efficient flocculant-producing strains was designed and tested. The results showed that this model for screening efficient flocculant-producing strains is very reliable and can greatly shorten the screening period. 13 flocculant-producing strains were isolated from activated sludge by conventional method. A strain, designated as HHE6, produced the bioflocculant with the turbidity removal 98% for kaolin suspension. Six of 13 strains selected as the original strains were treated with NTG as mutagen, and five mutant strains (HHE-P7, HHE-A8, HHE-P21, HHE-P24, HHE-A26) with high flocculation efficiency was obtained by selection, which exhibited the flocculation rate for kaolin suspension above 90%. Strains HHE6, HHE-P7, and HHE-P24 were classified as Penicillium purpurogenum, HHE-P21 as Penicillium cyclopium, HHE-A26 as Aspergillus versicolor and HHE-A8 as Aspergillus fumigatus, and it is hitherto unreported for biofloccutant-producing strains of Penicillium. The growth of the six strains (HHE6, HHE-P7, HHE-A8, HHE-P21, HHE-P24, HHE-A26) had similar curves, i.e. firstly increasing rapidly, keeping relatively constant then and finally decreasing gradually with cultivation time. The production of bioflocculants by strains showed the similar pattern to strain growth.

Bacteria↗