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At least 595 records · Page 33Linked to original sources
PubMed1989

A new procedure for the targeted inactivation of essential bacterial genes.

A new method is described for the exchange of a plasmid encoded mutant gene with its chromosomal counterpart. The method is based on positive selection and is applicable for the exchange of essential genes. The main features of the method are: (1) cloning of an antibiotic resistance marker (without its promoter) downstream of the cloned target gene, thus forming an artificial operon; (2) inactivating the target gene (and consequently also the antibiotic resistance gene) by inserting a strong transcriptional termination signal into it; and (3) selection for double recombinants by means of the antibiotic resistance gene.

Blotting, Southern↗
PubMed2001

[The association between SA gene and essential hypertension in Han Chinese].

OBJECTIVE: To evaluate the linkage of SA gene locus to essential hypertension(EH) in affected Han Chinese sib pairs and to ascertain the association of SA gene CT79 polymorphism with essential hypertension in Han Chinese hypertensives. METHODS: In Han Chinese at Shanghai, 96 random individuals, 80 essentially hypertensive sib pairs with hypertensive family history, 200 essential hypertensives with hypertensive family history and 200 normotensive control(NC) subjects without such family history were enrolled in these serial studies. MF-PCR-SSCP technique was applied to detect the frequency distributions of SA gene microsatellite D16S3046, D16S3136 and D16S3068. The linkage of SA gene locus to essential hypertension was analyzed by Green's IBS for affected siblings. SA gene variant was screened by PCR-SSCP- silver staining and confirmed by DNA sequencing, then an association study was performed to determine whether such variant was associated with essential hypertension. RESULTS: The frequency distributions of SA gene microsatellites D16S3046, D16S3136 and D16S3068 were of high polymorphism. The polymorphism information contents of D16S3046, D16S3136 and D16S3068 were 0.86, 0.82 and 0.80, and the heterozygosities 0.88, 0.71 and 0.77. The linkage of SA gene locus to essential hypertension was not observed; the linkage analysis t values of D16S3046,D16S3136 and D16S3068 were 0.972, 0.622 and 0.236, and the P values 0.384, 0.543 and 0.871, respectively. The C two head right arrow T substitution was confirmed, but there was no association of such variant with essential hypertension. The frequency distributions of genotypes and alleles in the hypertensive group were not significantly different from those in the normotensive group (P>0.05). CONCLUSION: SA gene is not linked to or associated with essential hypertension in Han Chinese. SA gene may not be a susceptible gene contributing to the development of essential hypertension in Han Chinese.

Adult↗
PubMed1992

The complete DNA sequence of yeast chromosome III.

The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

Base Sequence↗
PubMed2001

Molecular genetic dissection of TAF25, an essential yeast gene encoding a subunit shared by TFIID and SAGA multiprotein transcription factors.

We have performed a systematic structure-function analysis of Saccharomyces cerevisiae TAF25, an evolutionarily conserved, single-copy essential gene which encodes the 206-amino-acid TAF25p protein. TAF25p is an integral subunit of both the 15-subunit general transcription factor TFIID and the multisubunit, chromatin-acetylating transcriptional coactivator SAGA. We used hydroxylamine mutagenesis, targeted deletion, alanine-scanning mutagenesis, high-copy suppression methods, and two-hybrid screening to dissect TAF25. Temperature-sensitive mutant strains generated were used for coimmunoprecipitation and transcription analyses to define the in vivo functions of TAF25p. The results of these analyses show that TAF25p is comprised of multiple mutable elements which contribute importantly to RNA polymerase II-mediated mRNA gene transcription.

Amino Acid Sequence↗
PubMed1992

RAD25 (SSL2), the yeast homolog of the human xeroderma pigmentosum group B DNA repair gene, is essential for viability.

Xeroderma pigmentosum (XP) patients are extremely sensitive to ultraviolet (UV) light and suffer from a high incidence of skin cancers, due to a defect in nucleotide excision repair. The disease is genetically heterogeneous, and seven complementation groups, A-G, have been identified. Homologs of human excision repair genes ERCC1, XPDC/ERCC2, and XPAC have been identified in the yeast Saccharomyces cerevisiae. Since no homolog of human XPBC/ERCC3 existed among the known yeast genes, we cloned the yeast homolog by using XPBC cDNA as a hybridization probe. The yeast homolog, RAD25 (SSL2), encodes a protein of 843 amino acids (M(r) 95,356). The RAD25 (SSL2)- and XPBC-encoded proteins share 55% identical and 72% conserved amino acid residues, and the two proteins resemble one another in containing the conserved DNA helicase sequence motifs. A nonsense mutation at codon 799 that deletes the 45 C-terminal amino acid residues in RAD25 (SSL2) confers UV sensitivity. This mutation shows epistasis with genes in the excision repair group, whereas a synergistic increase in UV sensitivity occurs when it is combined with mutations in genes in other DNA repair pathways, indicating that RAD25 (SSL2) functions in excision repair but not in other repair pathways. We also show that RAD25 (SSL2) is an essential gene. A mutation of the Lys392 residue to arginine in the conserved Walker type A nucleotide-binding motif is lethal, suggesting an essential role of the putative RAD25 (SSL2) ATPase/DNA helicase activity in viability.

Amino Acid Sequence↗
PubMed1991

Isolation of a herpes simplex virus type 1 mutant deleted for the essential UL42 gene and characterization of its null phenotype.

We isolated a cell line, designated V9, stably transformed with the herpes simplex virus type 1 (HSV-1) UL42 gene, which is one of seven genes required in trans for the replication of plasmids containing an HSV origin of replication (C. A. Wu, N. J. Nelson, D. J. McGeoch, and M. D. Challberg, J. Virol. 62:435-443, 1988). V9 cells inducibly expressed the product of the UL42 gene, the 65-kDa DNA-binding protein (65KDBP), and were used as a permissive host to construct a mutant virus deleted for this essential gene. The UL42 deletion mutant, designated Cgal delta 42, displayed a tight early phenotype in nonpermissive Vero cells producing no infectious progeny, viral DNA, or late gene products but accumulated selected immediate-early and early transcripts with kinetics similar to those of wild-type virus. Wild-type levels of viral DNA and infectious progeny were produced in permissive V9 cells, despite the fact that V9 cells infected with Cgal delta 42 accumulated less than 1% of the UL42 RNA and protein found in Cgal+ virus-infected V9 or Vero cells. These results indicate that only small quantities of the 65KDBP are required for the synthesis of HSV DNA and the production of infectious virus. Although we could find no evidence that the superinduction of the 65KDBP in V9 cells infected with Cgal+ repressed expression of HSV-1 genes as observed in cells expressing another DNA-binding protein, ICP8 (P. K. Orberg and P. A. Schaffer, J. Virol. 61:1136-1146, 1987), the induction of the 65KDBP in V9 cells correlated with an approximately 2-h-earlier shift in the expression of genes from all three kinetic classes. The availability of the UL42 mutant should facilitate the construction of more subtle UL42 mutants which will be useful in the elucidation of the interrelationship between the 65KDBP and other DNA replication proteins as well as in the characterization of additional important functional domains.

Animals↗
PubMed1997

QSR1, an essential yeast gene with a genetic relationship to a subunit of the mitochondrial cytochrome bc1 complex, codes for a 60 S ribosomal subunit protein.

QSR1 (quinol-cytochrome c reductase subunit-requiring) is a highly conserved, essential gene in Saccharomyces cerevisiae that was identified through a synthetic lethal screen by its genetic relationship to QCR6, the gene for subunit 6 (Qcr6p) of the mitochondrial cytochrome bc1 complex. The function of the QSR1-encoded protein (Qsr1p) and its relationship to the QCR6-encoded protein are unknown. When yeast cell lysates are fractionated by density gradient centrifugation, Qsr1p separates from organelles and sediments with a uniformly sized population of particles that are similar to eukaryotic ribosomes upon velocity gradient centrifugation. When 40 S and 60 S ribosomal subunits are separated on velocity gradients, Qsr1p is found exclusively with the 60 S subunits, where it is a stoichiometric component. Extracts prepared from qsr1-1 cells are defective in in vitro translation assays relative to the wild type. In yeast cell lysates in which QCR6 rescues an otherwise lethal qsr1-1 mutation, Qcr6p is found only in mitochondria, both in respiratory-competent cells and in rho0 cells in which the bc1 complex is no longer present. These results suggest that suppression of the qsr1-1 mutation by QCR6 occurs by a trans-relationship across the outer mitochondrial membrane.

Electron Transport Complex III↗
PubMed1997

Mapping of a familial essential tremor gene, FET1, to chromosome 3q13.

Essential tremor (ET), the most common movement disorder in humans, appears to be inherited as an autosomal dominant trait in many families. The familial form is called familial essential tremor (FET), which seems similar to sporadic essential tremor. ET is a cause of substantial disability, particularly in the elderly. The prevalence of Parkinson's disease and dystonia may be increased in families with ET, but other movement disorders are seldom encountered in these families. Here we report the results of a genome-wide scan for FET genes in 16 Icelandic families with 75 affected individuals, in whom FET was apparently inherited as a dominant trait. The scan, which was performed with a 10-cM framework map, revealed one locus on chromosome 3q13 to which FET mapped with a genome-wide significance when the data were analysed either parametrically, assuming an autosomal dominant model (lod score = 3.71), or non-parametrically (NPL Z score = 4.70, p < 6.4 x 10(-6).

Chromosome Mapping↗
PubMed2006

Multiple knockout analysis of genetic robustness in the yeast metabolic network.

Genetic robustness characterizes the constancy of the phenotype in face of heritable perturbations. Previous investigations have used comprehensive single and double gene knockouts to study gene essentiality and pairwise gene interactions in the yeast Saccharomyces cerevisiae. Here we conduct an in silico multiple knockout investigation of a flux balance analysis model of the yeast's metabolic network. Cataloging gene sets that provide mutual functional backup, we identify sets of up to eight interacting genes and characterize the 'k robustness' (the depth of backup interactions) of each gene. We find that 74% (360) of the metabolic genes participate in processes that are essential to growth in a standard laboratory environment, compared with only 13% previously found to be essential using single knockouts. The genes' k robustness is shown to be a solid indicator of their biological buffering capacity and is correlated with both the genes' environmental specificity and their evolutionary retention.

Computer Simulation↗
PubMed1998

A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools.

In Saccharomyces cerevisiae, MEC1 and RAD53 are essential for cell growth and checkpoint function. Their essential role in growth can be bypassed by deletion of a novel gene, SML1, which functions after several genes whose overexpression also suppresses mec1 inviability. In addition, sml1 affects various cellular processes analogous to overproducing the large subunit of ribonucleotide reductase, RNR1. These include effects on mitochondrial biogenesis, on the DNA damage response, and on cell growth. Consistent with these observations, the levels of dNTP pools in sml1 delta strains are increased compared to wild-type. This effect is not due to an increase in RNR transcription. Finally, both in vivo and in vitro experiments show that Sml1 binds to Rnr1. We propose that Sml1 inhibits dNTP synthesis posttranslationally by binding directly to Rnr1 and that Mec1 and Rad53 are required to relieve this inhibition.

Amino Acid Sequence↗
PubMed1999

The Rhizobium etli trpB gene is essential for an effective symbiotic interaction with Phaseolus vulgaris.

A mutant strain (CTNUX4) of Rhizobium etli carrying Tn5 unable to grow with ammonium as the sole nitrogen source was isolated and characterized. Sequence analysis showed that Tn5 is inserted into a trpB (tryptophan synthase)-homologous gene. When tested on the roots of Phaseolus vulgaris, strain CTNUX4 was able to induce only small, slightly pink, ineffective (Fix-) nodules. However, under free-living conditions, strain CTNUX4 was unable to produce flavonoid-inducible lipo-chitin oligosaccharides (Nod factors) unless tryptophan was added to the growth medium. These data and histological observations indicate that the lack of tryptophan biosynthesis affects the symbiotic behavior of R. etli.

Amino Acid Sequence↗
PubMed2006

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets.

We present the first analysis of the human proteome with regard to interactions between proteins. We also compare the human interactome with the available interaction datasets from yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans) and fly (Drosophila melanogaster). Of >70,000 binary interactions, only 42 were common to human, worm and fly, and only 16 were common to all four datasets. An additional 36 interactions were common to fly and worm but were not observed in humans, although a coimmunoprecipitation assay showed that 9 of the interactions do occur in humans. A re-examination of the connectivity of essential genes in yeast and humans indicated that the available data do not support the presumption that the number of interaction partners can accurately predict whether a gene is essential. Finally, we found that proteins encoded by genes mutated in inherited genetic disorders are likely to interact with proteins known to cause similar disorders, suggesting the existence of disease subnetworks. The human interaction map constructed from our analysis should facilitate an integrative systems biology approach to elucidating the cellular networks that contribute to health and disease states.

Animals↗
PubMed2003

The plastid clpP1 protease gene is essential for plant development.

Plastids of higher plants are semi-autonomous cellular organelles that have their own genome and transcription-translation machinery. Examples of plastid functions are photosynthesis and biosynthesis of starch, amino acids, lipids and pigments. Plastid functions are encoded in approximately 120 plastid genes and approximately 3,000 nuclear genes. Although many embryo and seedling lethal nuclear genes are required for chloroplast biogenesis, until now deletion of plastid genes either had no phenotypic consequence (8 genes), or caused a mutant phenotype but did not affect viability (13 genes). Here we identify an essential plastid gene. By using the CRE-lox site-specific recombination system we have deleted clpP1 (caseinolytic protease P1), one of the three genes (clpP1, ycf1 and ycf2) whose disruption had previously only been possible in a fraction of the 1,000-10,000 plastid genome copies in a cell. Loss of the clpP1 gene product, the ClpP1 protease subunit, results in ablation of the shoot system of tobacco plants, suggesting that ClpP1-mediated protein degradation is essential for shoot development.

Endopeptidases↗
PubMed2007

Expression of the htrB gene is essential for responsiveness of Salmonella typhimurium and Campylobacter jejuni to harsh environments.

In Campylobacter jejuni, an htrB homologous gene is located in the lipo-oligosaccharide synthesis gene cluster. This study examined the effects of htrB expression on the responsiveness of Salmonella typhimurium and C. jejuni to harsh environments. Complementation experiments showed that the C. jejuni htrB gene could restore the normal morphology of the Salmonella htrB mutant, and its ability to grow without inhibition under heat, acid and osmotic stresses, but not bile stress. This indicated that the htrB genes in C. jejuni and S. typhimurium exhibit similar pleiotropic effects. Moreover, quantitative real-time RT-PCR showed that expression of the C. jejuni htrB gene was upregulated under acid, heat, oxidative and osmotic stresses, but did not change under bile stress. This indicated that the C. jejuni htrB gene plays a role in regulating cell responses to various environmental changes. Furthermore, deletion mutation of the htrB gene in C. jejuni was lethal, indicating that the htrB gene is essential for C. jejuni survival. Therefore, these results showed that expression of the htrB gene is essential for the response of S. typhimurium and C. jejuni to environmental stresses.

Acids↗
PubMed2004

KlSEC53 is an essential Kluyveromyces lactis gene and is homologous with the SEC53 gene of Saccharomyces cerevisiae.

Phosphomannomutase (PMM) is a key enzyme, which catalyses one of the first steps in the glycosylation pathway, the conversion of D-mannose-6-phosphate to D-mannose-1-phosphate. The latter is the substrate for the synthesis of GDP-mannose, which serves as the mannosyl donor for the glycosylation reactions in eukaryotic cells. In the yeast Saccharomyces cerevisiae PMM is encoded by the gene SEC53 (ScSEC53) and the deficiency of PMM activity leads to severe defects in both protein glycosylation and secretion. We report here on the isolation of the Kluyveromyces lactis SEC53 (KlSEC53) gene from a genomic library by virtue of its ability to complement a Saccharomyces cerevisiae sec53 mutation. The sequenced DNA fragment contained an open reading frame of 765 bp, coding for a predicted polypeptide, KlSec53p, of 254 amino acids. The KlSec53p displays a high degree of homology with phosphomannomutases from other yeast species, protozoans, plants and humans. Our results have demonstrated that KlSEC53 is the functional homologue of the ScSEC53 gene. Like ScSEC53, the KlSEC53 gene is essential for K. lactis cell viability. Phenotypic analysis of a K. lactis strain overexpressing the KlSEC53 gene revealed defects expected for impaired cell wall integrity.

Amino Acid Sequence↗
PubMed1997

Association analysis of TG repeat polymorphism of the neuronal nitric oxide synthase gene with essential hypertension.

The nitric oxide synthase (NOS) gene is thought to be involved in essential hypertension because nitric oxide is implicated in endothelium-mediated or nitroxidergic neuron-mediated vasodilation. Using simple tandem repeat DNA polymorphism of the neuronal constitutive NOS (nNOS) gene, we carried out an association study in patients with essential hypertension. One hundred and thirty-one patients with essential hypertension and 147 subjects with normal blood pressure were studied. Polymerase chain reaction was applied to amplify the TG repeat site in the nNOS gene, and alleles based on the TG repeat number were determined. Eight alleles were identified in this study of Japanese subjects. Overall distributions of allele frequencies in the two groups were not significantly different. Thus, the genes detected by examination of this microsatellite polymorphism in the nNOS gene are not associated with essential hypertension.

DNA↗
PubMed1993

Three adjacent genes of African swine fever virus with similarity to essential poxvirus genes.

Nucleotide sequencing of the right end of the SalIj fragment of the highly virulent Malawi Lil20/1 strain of African swine fever virus (ASFV) has revealed three adjacent genes with similarity to: serine-threonine protein kinases; members of the putative helicase superfamily SF2; and the vaccinia virus 56 kDa abortive late protein. All three genes are transcribed to the left with respect to the orientation of the ASFV genome. Gene L19IL predicts a protein similar to serine-threonine protein kinases including vaccinia virus gene B1R. Gene L19KL predicts a protein that is likely to be a nucleic acid-dependent ATPase, as it has similarity to both the poxvirus 70 kDa early transcription factor subunit and the poxvirus nucleoside triphosphatase I gene. Gene L19LL has extensive similarity to the vaccinia virus 56 kDa abortive late protein.

African Swine Fever Virus↗
PubMed1997

Sp1 recognition sites in the proximal promoter of the human vascular endothelial growth factor gene are essential for platelet-derived growth factor-induced gene expression.

Stimulation of NIH3T3 cells with platelet-derived growth factor (PDGF)-BB enhances expression of vascular endothelial growth factor (VEGF), an endothelial cell-specific mitogen and a key mediator of tumor angiogenesis. Here, we identified cis-acting VEGF promoter elements and trans-acting factors which are involved in PDGF-stimulated VEGF expression. By 5'-deletion and transient transfection analysis, a G + C-rich region at -85 to -50 of the human VEGF promoter was shown to be necessary and sufficient for both PDGF inducible and basal expression. The region contains three potential recognition sites for Sp1 transcription factors, which overlap with two Egr-1 sites. Mutations that abolish the ability of Sp1 to interact with the VEGF promoter element also abrogate expression induced by PDGF. Mutations of the potential Egr-1 binding sites did not affect PDGF responsiveness. Gel shift and antibody supershift analyses showed that Sp1 and Sp3 interact constitutively with the VEGF promoter element. Our data strongly suggest that enhanced VEGF gene expression in PDGF-induced NIH3T3 cells is mediated by Sp1 and/or Sp3 transcription factors bound to the -85 to -50 promoter region of the VEGF gene.

3T3 Cells↗