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Results for “gene function”

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At least 163 records · Page 9Linked to original sources

PubMed2001

Partial complementation of embryo defective mutations: a general strategy to elucidate gene function.

The EMB 506 gene has been characterised as essential for embryo development. To provide insights into the role of EMB 506, which is hidden by the embryo defective phenotype, the ABI3 promoter was fused to the EMB 506 cDNA. The expression of such a transgene should provide sufficient protein during embryogenesis to ensure normal embryo development in homozygous emb 506 seeds. We show that homozygous emb 506 seedlings, partially complemented with the ABI3::EMB 506 transgene, can be obtained. Most of the rescued emb 506 plants are able to flower and to set normal seeds, but show mild to severe depigmentation of rosette leaves and/or inflorescences. This effect on chloroplast development indicated a putative chloroplast localisation of the EMB 506 protein, which was demonstrated by GFP-protein fusion. However, EMB 506 cannot be considered as a chloroplast housekeeping protein only, since EMB 506 is not present in all photosynthetic tissues. This study demonstrates the power of this simple strategy, which could be widely applied to other emb mutants and which may reveal similar or additional roles for EMB genes at vegetative stages of the life cycle.

Arabidopsis↗

PubMed1981

Translational regulation: identification of the site on bacteriophage T4 rIIB mRNA recognized by the regA gene function.

The bacteriophage T4 gene regA encodes a protein that diminishes the expression of many unlinked early T4 genes. Previous work demonstrated that regA-mediated repression occurs after transcription. We report here on the identification of the target site on one regA-sensitive mRNA, the message encoding the phage T4 rIIB protein. The target for regA-mediated action overlaps the translational initiation domain of the rIIB messenger. The regA protein may be a repressor that operates translationally on a significant and interesting set of early phage T4 mRNAs.

Base Sequence↗

PubMed1997

The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs.

The particulate methane monooxygenase gene pmoA, encoding the 27 kDa polypeptide of the membrane-bound particulate methane monooxygenase, was amplified by PCR from DNA isolated from a blanket peat bog and from enrichment cultures established, from the same environment, using methane as sole carbon and energy source. The resulting 525 bp PCR products were cloned and a representative number of clones were sequenced. Phylogenetic analysis of the derived amino acid sequences of the pmoA clones retrieved directly from environmental DNA samples revealed that they form a distinct cluster within representative PmoA sequences from type II methanotrophs and may originate from a novel group of acidophilic methanotrophs. The study also demonstrated the utility of the pmoA gene as a phylogenetic marker for identifying methanotroph-specific DNA sequences in the environment.

DNA Probes↗

PubMed1997

The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs.

The methanol dehydrogenase gene mxaF, encoding the large subunit of the enzyme, was amplified from the DNA of a number of representative methanotrophs, methyletrophs, and environmental samples by PCR using primers designed from regions of conserved amino acid sequence identified by comparison of three known sequences of the large subunit of methanol dehydrogenase. The resulting 550-bp PCR products were cloned and sequenced. Analysis of the predicted amino acid sequences corresponding to these mxaF genes revealed strong sequence conservation. Of the 172 amino acid residues, 47% were conserved among all 22 sequences obtained in this study. Phylogenetic analysis of these MxaF sequences showed that those from type I and type II methanotrophs form two distinct clusters and are separate from MxaF sequences of other gram-negative methylotrophs. MxaF sequences retrieved by PCR from DNA isolated from a blanket bog peat core sample formed a distinct phylogenetic cluster within the MxaF sequences of type II methanotrophs and may originate from a novel group of acidophilic methanotrophs which have yet to be cultured from this environment.

Alcohol Oxidoreductases↗

PubMed1990

Molecular structures and evolution of mouse isozyme genes functioning in the malate-aspartate shuttle.

To examine molecular mechanisms of transcription of mammalian isozyme genes functioning in the malate-aspartate shuttle and to observe structural and evolutionary relationships, we investigated gene organizations of cAspAT and mAspAT, and cMDH and mMDH, and isolated and characterized cDNAs and genomic DNAs for these isozymes in mice. The deduced amino acid sequences of mouse cAspAT and mAspAT showed about 47%, and those of mouse cMDH and mMDH, about 23% overall homology. Surprisingly, the homology between the mouse cMDH and thermophilic bacterial MDH, as well as the homology between the mouse mMDH and E. coli MDH, markedly exceeds the intraspecies sequence homology between mMDH and cMDH from mice. The first duplication of a common ancestral MDH gene should thus have occurred long before the emergence of the eukaryotic cells, and subsequently, the mammalian mMDH and E. coli MDH genes have evolved from one of the duplicates. The mammalian cMDH and Thermus flavus MDH genes have no doubt evolved from one of the other duplicates. Moreover, structural organizations of the two-pairs of isozyme genes indicated that introns antedate the divergence of these mitochondrial and cytosolic isozyme genes. The 5' ends of all four isozyme genes lacked the TATA and CAAT boxes characteristic of eukaryotic promoters but did contain G + C-rich sequences and multiple transcription-initiation sites. We found several highly conserved regions in the 5' flanking sequences between mAspAT and cAspAT, between mMDH and mAspAT, and between cMDH and cAspAT genes.

Animals↗

PubMed2000

Effects of exercise training on cardiac function, gene expression, and apoptosis in rats.

This study determined the effects of exercise training on cardiac function, gene expression, and apoptosis. Rats exposed to a regimen of treadmill exercise for 13 wk had a significant increase in cardiac index and stroke volume index and a concomitant decrease in systemic vascular resistance compared with both age-matched and body weight-matched sedentary controls in the conscious state at rest. In exercise-trained animals, there was no change in the expression of several marker genes known to be associated with pathological cardiac adaptation, including atrial natriuretic factor, beta-myosin heavy chain, alpha-skeletal and smooth muscle actins, and collagens I and III. Exercise training, however, produced a significant induction of alpha-myosin heavy chain, which was not observed in rats with myocardial infarction. No histological features of cardiac apoptosis were observed in the treadmill-trained rats. In contrast, apoptotic myocytes were detected in animals with myocardial infarction. In summary, exercise training improves cardiac function without evidence of cardiac apoptosis and produces a pattern of cardiac gene expression distinct from pathological cardiac adaptation.

Actins↗

PubMed2000

Functional gene testing of the Glu298Asp polymorphism of the endothelial NO synthase.

OBJECTIVES: To test whether the Glu298Asp polymorphism of the endothelial nitric oxide synthase (eNOS) gene is of functional relevance in humans by altering endothelium-dependent vasodilation. BACKGROUND: The Asp298 variant of the eNOS gene product has been associated with arterial hypertension, coronary artery disease and myocardial infarction. The pathogenetic mechanism has not yet been elucidated. Since endothelium-dependent vasodilation has been shown to be impaired in these disorders, we hypothesized that the Glu298Asp polymorphism of the eNOS gene influences endothelium-dependent vasodilation. METHODS: In 80 patients with normal or elevated cholesterol, endothelium-dependent and -independent vasodilation was assessed. Forearm blood flow was measured by plethysmography in response to intra-arterial (i.a.) infusion of 12 and 48 microg/min acetylcholine and 3.2 and 12.8 microg/min nitroprusside, respectively. NG-monomethyl-L-arginine (L-NMMA) in doses of 4, 8 and 16 micromol/min was infused to test basal nitric oxide (NO) production and release. Genomic DNA was extracted from blood samples to determine the Glu298Asp polymorphism of the eNOS gene at position 1917 G/T after BanII restriction. RESULTS: Baseline parameters (age, gender, blood pressure, body mass index, cholesterol level) were similar across the genotypes. Genotype frequencies did not deviate from the Hardy-Weinberg equilibrium. No differences in forearm blood flow to i.a. acetylcholine (average increase: + 554 +/- 371%), nitroprusside or L-NMMA infusion were found across the eNOS genotypes, neither for endothelium-dependent or endothelium-independent vasodilation, nor for basal NO production and release. Our sample size of n = 80 had a power of > 80% (beta = 0.20) with a P value < 0.05 (alpha = 0.05) to detect a 200% difference in forearm blood flow response to 48 microg/min acetylcholine. CONCLUSIONS: At a power of 80%, we can exclude a relevant effect on endothelium-dependent vasodilation due to the eNOS Glu298Asp polymorphism. Thus, our functional genetic study does not suggest any biological effect of the eNOS Glu298Asp genotype on the cardiovascular system via an influence on endothelium-dependent vasodilation.

Adult↗

PubMed1982

Influence of phage T3 and T7 gene functions on a type III(EcoP1) DNA restriction-modification system in vivo.

The ocr+ gene function (gp 0.3) of bacteriophages T3 and T7 not only counteracts type I (EcoB, EcoK) but also type III restriction endonucleases (EcoP1). Despite the presence of recognition sites, phage DNA as well as simultaneously introduced plasmid DNA are protected by ocr+ expression against both the endonucleolytic and the methylating activities of the EcoP1 enzyme. Nevertheless, the EcoP1 protein causes the exclusion of T3 and T7 in P1-lysogenic cells, apparently by exerting a repressor-like effect on phage gene expression. T3 which induces an S-adenosylmethionine hydrolase is less susceptible to the repressor effect of the SAM-stimulated EcoP1 enzyme. The abundance of EcoP1 recognition sites in the T7 genome is explained by their near identity with the T7 DNA primase recognition site.

DNA Replication↗

PubMed1995

The age-1 and daf-2 genes function in a common pathway to control the lifespan of Caenorhabditis elegans.

Recessive mutations in two genes, daf-2 and age-1, extend the lifespan of Caenorhabditis elegans significantly. The daf-2 gene also regulates formation of an alternative developmental state called the dauer. Here we asked whether these two genes function in the same or different lifespan pathways. We found that the longevity of both age-1 and daf-2 mutants requires the activities of the same two genes, daf-16 and daf-18. In addition, the daf-2(e1370); age-1(hx546) double mutant did not live significantly longer than the daf-2 single mutant. We also found that, like daf-2 mutations, the age-1(hx546) mutation affects certain aspects of dauer formation. These findings suggest that age-1 and daf-2 mutations do act in the same lifespan pathway and extend lifespan by triggering similar if not identical processes.

Animals↗

PubMed2002

Analysis of gene function in somatic mammalian cells using small interfering RNAs.

RNA interference (RNAi) is a highly conserved gene silencing mechanism that uses double-stranded RNA (dsRNA) as a signal to trigger the degradation of homologous mRNA. The mediators of sequence-specific mRNA degradation are 21- to 23-nt small interfering RNAs (siRNAs) generated by ribonuclease III cleavage from longer dsRNAs. Twenty-one-nucleotide siRNA duplexes trigger specific gene silencing in mammalian somatic cells without activation of the unspecific interferon response. Here we provide a collection of protocols for siRNA-mediated knockdown of mammalian gene expression. Because of the robustness of the siRNA knockdown technology, genomewide analysis of human gene function in cultured cells has now become possible.

Animals↗

PubMed1995

Analysis of gene function in Dictyostelium.

Over the past ten years, powerful molecular genetic techniques have been developed to analyze gene function in Dictyostelium. DNA-mediated transformation using a variety of selections and vectors has allowed the introduction of wild-type or modified genes that are under various forms of transcriptional control. Homologous recombination is efficient and can be used to modify the genome in precise ways. In addition, it is now possible to clone genes based on their mutant phenotype alone, either by insertional mutagenesis, or by screening antisense expression cDNA libraries. Finally, a nearly complete physical map of the genome is available and so genes are easily mapped by physical techniques. We discuss many of these advances within the context of major research problems presently under study.

Animals↗

PubMed1985

Bacteriophage T4 unf (=alc) gene function is required for late replication in the presence of plasmid pR386.

The bacteriophage T4 unf gene, known to be involved in the arrest of transcription from cytosine-containing DNA, is unessential except in Escherichia coli strains containing plasmid pR386. Comparative genetic and biochemical analyses of parameters of unf+ and unf- phage growth in host cells isogenic except for the presence or absence of plasmid pR386 have shown that unf gene function is required for late phage DNA synthesis in the presence of the plasmid. Shutoff of host DNA, RNA, and protein syntheses, degradation of host DNA, adsorption, injection, and early phage DNA, RNA, and protein syntheses all occurred with normal or near-normal kinetics in unf- infections, even in the presence of the plasmid. The switch from early to late protein synthesis occurred in plasmid pR386-containing cells infected with unf+ or unf- phage. However, this switchover was slow in both cases and may be slower in unf- infections than in unf+ infections. Net incorporation of [3H]thymidine terminated at about 30 min after infection of pR386-containing cells with unf- phage at 30 degrees C. Alkaline sucrose gradient studies of the intracellular pools of replicative DNA in unf-infected plasmid pR386-containing cells indicated that this DNA is not detectably nickel or cleaved at the time that DNA synthesis aborts. The addition of chloramphenicol subsequent to early enzyme synthesis prevented the arrest of DNA synthesis in plasmid-containing cells infected with unf-phage.

Centrifugation, Density Gradient↗

PubMed2003

Predicting gene function by conserved co-expression.

We show that gene co-expression, which generally provides only a very weak signal for the prediction of functional interactions, can provide a reliable signal by exploiting evolutionary conservation. The encoded proteins of conserved co-expressed gene pairs are highly likely to be part of the same pathway not only after speciation (98%), but also after parallel gene duplication (97%). Conserved co-expression combined with homology data enables us to predict specific gene functions. The use of conservation between parallel duplicated gene pairs to predict function is especially promising given that gene duplication is common in eukaryotes, and that data from only a single organism can be used.

Animals↗

PubMed1999

Antisense oligonucleotides: a systematic high-throughput approach to target validation and gene function determination.

Antisense technology provides a high-throughput and systematic approach to drug target validation and gene function discovery. In combination with other emerging technologies (such as microarrays), this technology will enable efficient evaluation of the sequence data generated by the Human Genome Project. The authors review recent advances in the antisense field and discuss the potential use of antisense technology for functional genomics.

Journal Article↗

PubMed1982

PEP4 gene function is required for expression of several vacuolar hydrolases in Saccharomyces cerevisiae.

The pep4-3 mutation results in a 90-95% reduction in the levels of five vacuolar hydrolases in yeast, including proteinases A and B, carboxypeptidase Y, RNase(s) and the repressible alkaline phosphatase. The mutation is without effect on two secreted glycoproteins, on an enzyme of the vacuolar membrane, and on a proteinase located outside of the vacuole. Mutations at the PEP4 locus exhibit a dosage effect on the levels of some, but not all, of the enzymes whose expression requires the function of the gene.

Alkaline Phosphatase↗

PubMed1996

Paralogous Hox genes: function and regulation.

The Hox homeobox gene family plays a pivotal role in regulating patterning and axial morphogenesis in vertebrates. Molecular characterization of the four Hox clusters has shown that they are evolutionarily related with respect to sequence, organization, and expression, suggesting they arose by duplication and divergence. Transgenic analysis has clearly demonstrated the functional roles of individual genes in a broad range of embryonic tissues, and in compound mutants has addressed the issues of cooperativity and redundancy. There is an emerging picture of the cis-regulatory elements underlying Hox expression, and for the 3' members of the clusters there is a considerable degree of conservation between paralogous genes with respect to their functional roles and regulatory control.

Animals↗

PubMed2001

Quantifying functional gene populations: comparing gene abundance and corresponding enzymatic activity using denitrification and nitrogen fixation in pulp and paper mill effluent treatment systems.

The relationship between the abundance of three functional genes and their corresponding biochemical reaction rates was investigated in several activated sludge and mill effluent microbial communities. Gene probes were prepared for two key denitrification genes (nirS and nirK) and for one nitrogen-fixation gene (nifH) and were validated using a variety of strains of known nir and nif genotype. ATP-based measures of viable cell numbers were used to provide total population sizes. In certain microbial communities (activated sludge enrichment cultures and multiple samples taken from the same mill primary clarifier), a strong correlation was observed between gene abundance and biochemical activity rates. However, when comparing several different nonenriched activated sludge bioreactors and separate primary clarifier microbial communities, the ratio of specific gene abundance to biochemical activity rates varied widely. These results suggest that in cases where a microbial community is not fully induced for a given biochemical activity or when very different communities are compared, quantitative gene probing can give a better measure of a community's potential to carry out the encoded function than can the relevant biochemical assay. However, the gene quantitation method employed here probably underestimated the true number of probed genes present in the microbial communities due to nirS and nifH genes in the communities having reduced DNA sequence similarity with the probes used.

Adenosine Triphosphate↗

PubMed2000

MHC class I-subversive gene functions of cytomegalovirus and their regulation by interferons-an intricate balance.

Multiple glycoproteins of human cytomegalovirus (HCMV) encoded by the genes US2, US3, US6 and US11 interrupt the MHC class I pathway of antigen presentation at distinct checkpoints to avoid recognition of infected cells by cytotoxic CD8+ T lymphocytes. The action of cytokines like interferon (IFN)-gamma, IFN-alpha/beta and tumour necrosis factor alpha (TNF-alpha) compensate for the viral inhibition and restore antigen presentation in HCMV-infected cells. This finding was explained by their effects on cellular rather than viral genes and reflected by an increase in the production, assembly and maturation of MHC class I molecules resulting in an escape of MHC I from viral control. Here we reproduce the IFN-gamma-mediated effect when MHC I-subversive gene functions of HCMV are tested in isolation, but the efficacy of IFN-gamma to restore MHC I surface expression in US2-, US6- and US11-transfectants differs significantly. In addition, in HCMV-infected cells IFN-gamma strongly affects the synthesis of the US6-encoded glycoprotein. Despite the capability of HCMV to block the interferon signaling pathway the IFN-gamma driven enhancement of MHC class I and class II expression remains effective provided that cells are exposed to IFN-gamma before infection. Our findings illustrate a complex interplay between host immune factors and viral immune evasion functions.

Amino Acid Sequence↗