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At least 19 recordsLinked to original sources
PubMed1978

Relationship between gene function and gene location in Escherichia coli.

Genes of Escherichia coli were grouped according to the "biochemical relatedness" of the enzymes they specifiy, using two schemes to determine relatedness: similarity of reaction or similarity of reactants. The tendency of biochemically related genes as so defined to lie approximately 90 degrees or 180 degrees from one another on the circular genetic map was analyzed statistically. Of the classes analyzed, only the genes for the enzymes of glucose catabolism showed a significant departure from random distribution in this respect. The glucose catabolism genes showed a pronounced tendency to lie either 90 degrees of 180 degrees from one another (P = ca. 10(-9)), and, furthermore, most of these genes were found to lie in only four gene clusters on the E. coli genome. The significance of this observation is discussed in relation to evolutionary mechanisms and to mechanisms of gene expression.

Amino Acids↗
PubMed1992

Antisense oligodeoxynucleotides as probes of T-lymphocyte gene function.

Conventional and thiophosphonate-derivatized oligonucleotides were employed to specifically regulate functional gene expression in murine T-cell hybridomas. For example, induction of apoptotic cell death following activation of T-cell hybridomas was examined using antisense oligonucleotides corresponding to several protooncogenes. We found that antisense oligodeoxynucleotides corresponding to c-myc inhibited both the characteristic DNA fragmentation and the loss of cell viability following activation without affecting production of lymphokines. Functional antisense oligonucleotides corresponding to c-fos had no effect in this system. These results demonstrate the use of antisense oligonucleotides to regulate function in T-cell hybridomas and provide valuable insights into the molecular bases of this biological phenomenon. Antisense oligonucleotides were also used to study another problem, the relation of T-cell-derived antigen-specific immunoregulatory factors to the T-cell receptor (TCR). Because the translation start of each TCR gene usually varies from one T cell to another, antisense oligonucleotides corresponding to the TCR V alpha or V beta of different cells were shown to act in a cell-specific manner. Furthermore, this method was used to demonstrate that a soluble antigen-specific regulatory activity produced by one of the T-cell lines depends on expression of the specific TCRa, an observation that has since been confirmed by gene transfer experiments. Expression of the CD3-TCR complex on the cell surface was also blocked by antisense oligonucleotides corresponding to CD3 gamma and CD3 zeta; however, neither these nor TCR V beta antisense oligonucleotides had any effect on production of the soluble regulatory activity.

Animals↗
PubMed1989

Cellular senescence involves stochastic processes causing loss of expression of differentiated function genes: transfection with SV40 as a means for dissociating effects of senescence on growth and on differentiated function gene expression.

In the accompanying work we demonstrated that the decline in expression of steroid 17 alpha-hydroxylase in mass cultures and clones of adrenocortical cells is the result of a stochastic switching process which yields mixtures of expressing and nonexpressing cells. There is an apparent positive correlation between the replicative potential of adrenocortical cell cultures and the number of cells in the culture that can express 17 alpha-hydroxylase. We investigated this by extending the cells' replicative potential by transfecting them with cloned SV40 virus. Cells from a senescent subclone, with very limited remaining replicative potential, were transfected. The cell population showed a progressive increase in growth rate and gave rise to a line of cells that expressed T antigen and which was apparently immortalized. Induction of mRNA for 17 alpha-hydroxylase by cyclic AMP was absent in this line of cells, as it was in the senescent cells prior to transfection. The cells remained responsive to gene induction by cyclic AMP as evidenced by increases in mRNA and activity for cholesterol side-chain cleavage. The absence of 17 alpha-hydroxylase expression in this line was not the result of interference by SV40 T antigen. When early passage cells were transfected with pSV3neo, which contains the early region of SV40 and neo, and were selected with G418, SV40 T antigen-expressing lines were derived which showed high levels of expression of 17 alpha-hydroxylase after induction with cyclic AMP. These cells maintained high levels of expression of 17 alpha-hydroxylase through four successive recloning events, over a period of replication much longer than that achievable by nontransfected cells. Thus, transfection by SV40 can be used to dissociate effects of senescence on growth and differentiated gene expression. T antigen expression selectively affects growth, but preserves the state of expression of a differentiated function gene as it was prior to transfection.

Adrenal Cortex↗
PubMed1992

Identification of a processed pseudogene related to the functional gene encoding the GM2 activator protein: localization of the pseudogene to human chromosome 3 and the functional gene to human chromosome 5.

The GM2 activator protein is an essential substrate cofactor for the hydrolysis of GM2 ganglioside by lysosomal beta-hexosaminidase A (EC 3.2.1.52). There have been conflicting reports as to the chromosomal localization of the gene encoding the activator. We demonstrate here that these conflicts were caused by the presence of a previously unidentified processed activator-pseudogene on chromosome 3, and we confirm a previous ELISA-based localization of the functional activator gene to chromosome 5. Our data indicate that the functional activator locus can still be considered a candidate site for defects causing some forms of spinal muscular atrophy.

Animals↗
PubMed1992

Use of gene replacement transformation to elucidate gene function in the qa gene cluster of Neurospora crassa.

Gene replacement by transformation, employing selective genetic recombination techniques, has been used to delete or disrupt the qa-x, qa-y and qa-1S genes of the qa gene cluster of Neurospora crassa. The growth characteristics of the strain carrying the deletion of the qa-y gene support earlier evidence that this gene encodes a quinic acid permease. The strain containing the deletion of the qa-1S gene (delta qa-1S) was examined with respect to quinic acid induction and carbon catabolite repression. The delta qa-1S strain exhibits constitutive expression of the qa genes supporting earlier evidence that the qa-1S gene codes for a repressor. Several of the qa genes continued to be expressed at high levels even in the presence of glucose in the delta qa-1S strain, which indicates that transcription of these genes is not being affected directly by a repressor molecule in the presence of glucose.

Chromosome Deletion↗
PubMed1979

An adenovirus type 5 early gene function regulates expression of other early viral genes.

We have identified an adenovirus type 5(Ad5) early gene function located in early region 1 which is required for the production of early cytoplasmic mRNAs corresponding to early regions 2, 3, and 4. Mutant dl312 (lacks the segment between 1.5 and 4.5 map units) grows as well as wild-type virus in 293 cells (Ad5-transformed human embryonic kidney cells), but its growth is severely restricted in HeLa cells. We detect no viral RNAs in the cytoplasm of dl312-infected HeLa cells. Viral RNA sequences are present, however, in dl312-infected HeLa cell nuclei.

Adenoviruses, Human↗
PubMed1978

The ocr gene function of bacterial viruses T3 and T7 prevents host-controlled modification.

On pre-infection of the host Escherichia coli B with u.v.-inactivated T3 or T7 phage able to express their early genes (like 0.3), B-specific modification of superinfecting, successfully multiplying viruses does not take place. The ocr gene function (gene 0.3) of T3 and T7 not only prevents host-specific DNA restriction but also modification, probably by inhibiting the same late step in the interaction between the restriction enzyme and DNA.

Coliphages↗
PubMed1975

Viral gene functions expressed and detected by temperature-sensitive mutants of herpes simplex virus.

The expression of HSV-specific gene functions by 22 ts mutants of HSV-1 in 15 complementation groups and 8 ts mutants of HSV-2 in 7 complementation groups has been studied at the nonpermissive temperature. Four cistrons of HSV-1 and three cistrons of HSV-2 with defects in viral DNA and DAN polymerase synthesis were identified. DNA-mutants of HSV-1 revealed a greater alteration in HSV polypeptide synthesis and viral assembly than DNA- mutants of HSV-2. Mutants with apparent defects in structural proteins have been identified for both HSV-1 and HSV-2 as demonstrated by their increased themolability. The general organization of the provisional HSV-1 and HSV-2 linkage maps revealed a similarity in the arrangement of functionally related cistrons, with DNA- mutants being located on the left-hand side of each map and mutants with phenotypic properties similar to those of the wild-type virus, on the right-hand side. An early polypeptide of HSV (VP175, MW 175,000) was found to accumulate in cells infected at the nonpermissive temperature withts mutants of HSV-1 in complementation group B. The VP175 polypeptide was isolated from such cells by a combination of SDS-preparative and analytical disc gel electrophoresis. Antiserum prepared to this polypeptide was found to descriminate between HSV-1 and HSV-2 by immunofluorescence. On the other hand, type-specific gene functions of HSV-1 and HSV-2 were not demonstrated through intertypic complementation and recombination tests with heterologous mutant pairs, whereas mutually exchangeable or common gene functions were readily identified. Eight ts mutants of HSV-2 were used to detect functional HSV genes in hamster embryo cells transformed by HSV-2. Normal hamster cells and SV40-transformed hamster cells failed to support the replication of the mutants at the nonpermissive temperature. However, the replication of two mutants, defective in late functions, was significantly enhanced in two independently derived HSV-2-transformed cell lines. Thus functional HSV genetic information was detected in HSV-2-transformed cells through the use of ts mutants. Moreover, it appears that the information present in both cell lines is not only specific but involves late HSV functions.

Antigens, Viral↗
PubMed1975

Analysis of expression of the rII gene function of bacteriophage T4.

Temperature-sensitive (ts) mutants of the T4 phage rII gene were islated and used in temperature shift experiments that revelaed two different expressions for the normal rII (rII+) gene function in vivo: (i) an early expression (0 to 12 min postinfection at 30 C) that prevents restriction of T4 growth in Escherichia coli hosts lysogenic for gamma phage, and (ii) a later expression (12 to 18 min postinfection at 30 C) that results in restriction of T4 growth when the phage DNA ligase (gene 30) is missing. The earlier expression appeared to coincide with the period of synthesis of the protein product of the T4 rIIA cistron, whereas the later expression occurred after rIIA protein synthesis had stopped. The synthesis of the protein product of the rIIB cistron continues for several minutes after rIIA protein synthesis ceases (O'Farrell and Gold, 1973). The two rII+ gene expressions might require different molar ratios of the rIIA and rIIB proteins. It is possible that the separate expressions of rII+ gene function are manifestations of different associations between the two rII proteins and other T4-induced proteins that are synthesized or activated at different times after phage infection.

Coliphages↗
PubMed2026

XsiAMT1.1a was identified as a novel ammonium uptake functional gene and its overexpression combined with GA4 application significantly increased yield in Arabidopsis thaliana.

Nitrogen (N) is a key limiting factor for plant yield. Ammonium is one of the main N forms absorbed by plants. Overexpression of ammonium uptake functional genes, such as ammonium transporter (AMT), can increase yield. However, the AMTs reported to enhance yield significantly is still limited. No researches have focused on the effect of overexpressing AMT combined with hormone application on yield improvement. In this study, we first investigated the role of XsiAMT1.1a, a potential ammonium uptake functional gene in an ammonium preference plant Xanthium sibiricum, in ammonium uptake by the analysis of bioinformatics, gene expression and subcellular localization, and the determination of ammonium uptake rate in endogenous silencing and heterologous overexpression plants. Subsequently, the effect of XsiAMT1.1a overexpression combined with hormone application on yield increase was further investigated in model plant Arabidopsis thaliana. Our results showed that XsiAMT1.1a shared the same conserved domains with AtAMT1 subfamily members and localized on the plasma membrane. XsiAMT1.1a was induced by N deficiency and highly expressed during the reproductive period. XsiAMT1.1a endogenous silencing and heterologous overexpression significantly decreased and increased ammonium uptake rates in X. sibiricum and A. thaliana, respectively. Overexpression of XsiAMT1.1a significantly improved total N accumulation, biomass and yield in A. thaliana, while XsiAMT1.1a overexpression combined with GA4 application had a stronger promoting effect on the above indicators. Our research identified a novel ammonium uptake functional gene, XsiAMT1.1a, and provided a new yield-increasing strategy which was verified in A. thaliana.

Arabidopsis↗
PubMed1992

Autocatalysis and phenotypic expression of Drosophila homeotic gene Deformed: its dependence on polarity and homeotic gene function.

Previously published experiments have shown that the endogenous Dfd gene can be ectopically activated by its own (heat-shock-driven) product in a subset of cells of different segments. This results in the differentiation of maxillary structures like cirri and mouth hooks in places where they normally do not appear, and represents a phenomenon of autocatalysis of homeotic gene function that differs from the normal activation process. We show that this out-of-context activation occurs in cells belonging to the anterior compartments of the three thoracic and the A1 to A8 abdominal segments and that it requires the normal function of the polarity genes wingless (wg) and engrailed (en). The wg product, in addition to that of Dfd, appears to be sufficient to activate the endogenous Dfd gene in many embryonic cells. We have studied the effect of several homeotic genes on Dfd activation and phenotypic expression: Scr, Antp, Ubx and Abd-B repress Dfd both transcriptionally and at the phenotypic level, if their products are in sufficient amounts. The endogenous abd-A gene does not have a noticeable effect, but when it is replaced by an hsp70-abd-A gene, which produces a high and uniform level of expression, the phenotypic expression of Dfd is suppressed. Our results also suggest that the differentiation of cirri is induced by Dfd-expressing cells in non-expressing neighboring cells, and that this interaction occurs across the parasegmental border.

Animals↗
PubMed1989

Human non-histone chromosomal protein HMG-17: identification, characterization, chromosome localization and RFLPs of a functional gene from the large multigene family.

The multigene family of chromosomal protein HMG-17 is the largest known human retropseudogene family. A functional gene was identified and isolated by screening cDNA-selected genomic clones with a set of 5 oligonucleotides whose sequence corresponded to regions in which the sequence of the retropseudogenes differed from that of the cDNA and which did not span previously identified exon/intron junctions. A 7195 bp genomic fragment containing 6 exons, ranging in size from 30 to 817 bp, two of which encode the entire DNA binding domain of the protein, was sequenced. The gene has features which are typical to "housekeeping" genes and is characterized by a very high content of G + C residues in a 1.4 kb fragment starting 500 bp from the cap site and by an "HTF" island in the 5' region. Transcriptional regulatory signals, exon/intraon boundaries and features characteristic of "housekeeping" genes are evolutionary conserved between the human and chicken genes. The HMG-17 gene was localized to human chromosome 1p12-34. RFLP's useful for further mapping were detected. The experimental evidence presented leads to the assumption that the gene characterized is the only functional human HMG-17 gene.

Amino Acid Sequence↗
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↗
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↗
PubMed1990

Escherichia coli 4.5S RNA gene function can be complemented by heterologous bacterial RNA genes.

The essential 4.5S RNA gene of Escherichia coli can be complemented by 4.5S RNA-like genes from three other eubacteria, including both gram-positive and gram-negative organisms. Two of the genes encode RNAs similar in size to the E. coli species; the third, from Bacillus subtilis, specifies an RNA more than twice as large. The heterologous genes are expressed efficiently in E. coli, and the product RNAs resemble those produced by cognate cells. We conclude that the heterologous RNAs can replace E. coli 4.5S RNA and that the essential function of 4.5S RNA is evolutionarily conserved. A consensus structure is presented for the functionally related 4.5S RNA homologs.

Base Sequence↗
PubMed1990

[Methods of studying genes and gene function].

In several fields, such as immunology, biochemistry, and structural biology, but particularly in molecular genetics, modern methods enable genes and their protein products to be analysed and described. The tools are now available to study any physiological process or disease at the molecular level. As a result, genetic diseases and viral infections can be better identified and understood. Basic cellular and physiological mechanisms are beginning to be elucidated, the disturbance of which is a factor involved in cancerogenesis, for instance, or the development of hypercholesterolaemia. The article is intended as a brief review of current methods of studying genes and their function. The isolation and characterisation of genes by means of recombinant DNA technology, the identification of defective genes, and the analysis of gene function, both in vitro and in vivo are presented.

Chromosome Mapping↗
PubMed1991

Segmental exchange between MHC class I genes in a higher primate: recombination in the gorilla between the ancestor of a human non-functional gene and an A locus gene.

Classical human major histocompatibility complex (MHC) class I molecules are the products of highly diverse gene loci. It has been suggested that segmental exchange may play a role in the generation of diversity at the antigen recognition site of MHC class I molecules. Here we present the cloning, sequencing and expression of two gorilla A locus cDNAs. One of these cDNAs shows remarkable similarity to the non-functional HLA-AR locus gene (5.4-LBF) only in exon 2. The remainder of the cDNA, however, is most closely related to other classical higher primate A locus genes. This suggests that a segmental exchange may have occurred between the ancestor of the non-functional HLA-AR gene and a classical gorilla A locus gene. Furthermore, the recombination event resulting in Gogo-A3 has affected its antigen recognition site. These data, therefore, demonstrate that segmental exchange can generate diversity at the antigen recognition sites of primate MHC class I molecules and suggest that non-functional genes can contribute to the generation of diversity of classical MHC class I genes.

Animals↗