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PubMed1989

Negative control of cell division by mreB, a gene that functions in determining the rod shape of Escherichia coli cells.

Exponentially growing Escherichia coli cells containing additional copies of the shape-determining gene mreB were found to be elongated, whereas mreB mutant cells were spherical and overproduced penicillin-binding protein 3, a septum peptidoglycan synthetase. The effect of the mreB gene on expression of ftsI, the structural gene for penicillin-binding protein 3, was examined by using an ftsI-lacZ fusion gene on a plasmid. Formation of beta-galactosidase from the fusion gene was significantly increased in mreB129 mutant cells, and its overproduction was suppressed to a normal level by the presence of a plasmid containing the mreB gene. These results indicate a negative mechanism of control of cell division by this morphology gene and suggest that the gene functions in determining whether division or elongation of the cells occurs.

Cell Division↗
PubMed1995

[The change of gut barrier function and gene expression after surgical stress and parenteral nutrition].

Surgical stress and parenteral nutrition (PN) may cause gut mucosal atrophy and alter barrier function. Gene expression of growth factors and enzymes in small intestine may change. The effects of alanyl-glutamine dipeptide (Ala-Gln) on gut barrier and the gene expression of insulin-like factor I (IGF-I) and glutaminase in parenteral infusion rats with massive small intestine resection were investigated. Twenty Wistar rats were catheterized with 60% small bowel resectin. They were divided into two groups. Control group (n = 10) received traditional parenteral nutritional solution, and study group (n = 10) received Ala-Gln enriched nutritional solution (3% Ala-Gln). The rats were maintained with their respective diets for 7 days. The rats in the study group maintained serum glutamine concentration (844.0 +/- 13.2uMol: 640.4 +/- 17.2uMol, P < 0.05), mucosal architecture (mucosal thickness 591 +/- 12uM: 486 +/- 8uM, P < 0.05) and villus height (404 +/- 7uM: 303 +/- 5uM, P < 0.05). Bacterial translocation rate decreased in the study group (70%: 20%, P < 0.05). Ileal mucosal IGF-I mRNA and jejunal mucosal glutaminase mRNA in the study group increased twofold and threefold respectively. The results suggest that Ala-Gln may enhance gut growth and improve gut mucosa integrity and barrier function in part by means of stimulating IGF-I and glutaminase expression in surgical stress.

Animals↗
PubMed2006

Electrotransfer into skeletal muscle for protein expression.

An efficient and safe method to deliver DNA in vivo is a requirement for several purposes, such as study of gene function and gene therapy applications. Among the different non-viral delivery methods currently under investigation, in vivo DNA electrotransfer has proven to be one of the most efficient and simple. This technique is a physical method of gene delivery consisting in local application of electric pulses after DNA injection. Although this technique can be applied to almost any tissue of a living animal, including tumors, skin, liver, kidney, artery, retina, cornea or even brain, this review will focus on electrotransfer of plasmid DNA into skeletal muscle and its possible uses in gene therapy, vaccination, or functional studies. Skeletal muscle is a good target for electrotransfer of DNA as it is: a large volume easily accessible, an endocrine organ capable of expressing several local and systemic factors, and muscle fibres as post-mitotic cells have a long lifespan that allows long-term gene expression. In this review, we describe the mechanism of DNA electrotransfer, we assess toxicity and safety considerations related to this technique, and we focus on important therapeutic applications of electrotransfer demonstrated in animal models in recent years.

Animals↗
PubMed1993

Ets oncogene-related gene Elg functions in Drosophila oogenesis.

Members of the ets gene family encode transcription factors that regulate the expression of a variety of cellular and viral genes including several protooncogenes. We have utilized Drosophila to elucidate the in vivo function of one family member. We show by complementation rescue and sequence analysis that the female sterile mutant tiny eggs (tne) is an allele of the Drosophila Ets-related gene Elg (also called D-elg). The mutation of a highly conserved tyrosine residue in the ETS DNA-binding domain of the Elg gene product demonstrates that normal gene function is required for proper follicle cell migration, chorion formation, and nurse cell-chromosome decondensation during Drosophila oogenesis.

Amino Acid Sequence↗
PubMed2004

Functional evolution of the vertebrate Myb gene family: B-Myb, but neither A-Myb nor c-Myb, complements Drosophila Myb in hemocytes.

The duplication of genes and genomes is believed to be a major force in the evolution of eukaryotic organisms. However, different models have been presented about how duplicated genes are preserved from elimination by purifying selection. Preservation of one of the gene copies due to rare mutational events that result in a new gene function (neofunctionalization) necessitates that the other gene copy retain its ancestral function. Alternatively, preservation of both gene copies due to rapid divergence of coding and noncoding regions such that neither retains the complete function of the ancestral gene (subfunctionalization) may result in a requirement for both gene copies for organismal survival. The duplication and divergence of the tandemly arrayed homeotic clusters have been studied in considerable detail and have provided evidence in support of the subfunctionalization model. However, the vast majority of duplicated genes are not clustered tandemly, but instead are dispersed in syntenic regions on different chromosomes, most likely as a result of genome-wide duplications and rearrangements. The Myb oncogene family provides an interesting opportunity to study a dispersed multigene family because invertebrates possess a single Myb gene, whereas all vertebrate genomes examined thus far contain three different Myb genes (A-Myb, B-Myb, and c-Myb). A-Myb and c-Myb appear to have arisen by a second round of gene duplication, which was preceded by the acquisition of a transcriptional activation domain in the ancestral A-Myb/c-Myb gene generated from the initial duplication of an ancestral B-Myb-like gene. B-Myb appears to be essential in all dividing cells, whereas A-Myb and c-Myb display tissue-specific requirements during spermatogenesis and hematopoiesis, respectively. We now report that the absence of Drosophila Myb (Dm-Myb) causes a failure of larval hemocyte proliferation and lymph gland development, while Dm-Myb(-/-) hemocytes from mosaic larvae reveal a phagocytosis defect. In addition, we show that vertebrate B-Myb, but neither vertebrate A-Myb nor c-Myb, can complement these hemocyte proliferation defects in Drosophila. Indeed, vertebrate A-Myb and c-Myb cause lethality in the presence or absence of endogenous Dm-Myb. These results are consistent with a neomorphic origin of an ancestral A-Myb/c-Myb gene from a duplicated B-Myb-like gene. In addition, our results suggest that B-Myb and Dm-Myb share essential conserved functions that are required for cell proliferation. Finally, these experiments demonstrate the utility of genetic complementation in Drosophila to explore the functional evolution of duplicated genes in vertebrates.

Animals↗
PubMed2005

Moss (Physcomitrella patens) functional genomics--Gene discovery and tool development, with implications for crop plants and human health.

Recently, the moss Physcomitrella patens was established as a versatile tool in plant functional genomics. Mosses represent the oldest living clade of land plants, separated by approximately 450 million years of evolution from crop plants. Consequently, mosses contain metabolites and genes not known from these seed plants. In Physcomitrella, nuclear genes can be targeted by homologous recombination as efficiently as in yeast, allowing reverse genetics approaches in plants at high-throughput levels for the first time. Comprehensive expressed sequence tag databases gave new insights into the levels of diversity in land plants which are now ready to be exploited in plant biotechnology. In forward genetics screens, saturated tagged mutant collections help to unravel novel gene - function relationships. Additionally, proteomics tools are at hand to analyse subcellular proteomes, as well as the phosphoproteome, as the core of eukaryotic signal transduction. Moreover, specifically designed Physcomitrella strains can produce human therapeutic proteins safely and cost-effectively in bioreactors.

Bioreactors↗
PubMedDate not supplied

Cyclic GMP-dependent protein kinases: understanding in vivo functions by gene targeting.

Identifying the specific functions that are mediated by cyclic GMP (cGMP)-dependent protein kinases is key to our understanding of the biological role of the nitric oxide/cGMP signaling cascade. Over the last two decades, there have been numerous reports on the functional roles of cGMP kinases. However, most studies have been performed with isolated cells and organs by using specific activators and inhibitors of cGMP kinases. Under such experimental conditions, a clear dissection between the cGMP kinase pathway and other pathways, for example, that of cyclic AMP kinase, has been difficult to achieve. In order to identify biological processes in which cGMP kinases are unambiguously involved, the genes of cGMP kinase I and cGMP kinase II have been deleted in mice. This review focuses on the physiological functions that are regulated by cGMP kinases as revealed by cGMP kinase-deficient animals. For cGMP kinase I, these functions include the contractility of vascular and gastrointestinal smooth muscle and the homeostasis of platelet activity. According to its expression pattern, the Type II cGMP kinase plays a definite biological part in transepithelial Cl- and Na+ transport in the intestine, longitudinal growth of long bones, and the regulation of the kidney renin-angiotensin-aldosterone system. Further, cGMP kinase I and II mutants reveal new aspects for the role of nitric oxide/cGMP in the induction of neuronal plasticity, such as hippocampal long-term potentiation and cerebellar long-term depression. In conclusion, inactivation of the cGMP kinase genes shows that cGMP kinases regulate very specifically distinct cellular functions by pathways that are separate from those used by cyclic AMP kinases. Mice deficient in cGMP kinases exhibit severe defects and, therefore, may serve as animal models for several human diseases, including hypertension, thrombosis, gastrointestinal dysmotility, and dwarfism.

Animals↗
PubMed1999

Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase

Rice field soil with a nonsaturated water content induced CH4 consumption activity when it was supplemented with 5% CH4. After a lag phase of 3 days, CH4 was consumed rapidly until the concentration was less than 1.8 parts per million by volume (ppmv). However, the soil was not able to maintain the oxidation activity at near-atmospheric CH4 mixing ratios (i.e., 5 ppmv). The soil microbial community was monitored by performing denaturing gradient gel electrophoresis (DGGE) during the oxidation process with different PCR primer sets based on the 16S rRNA gene and on functional genes. A universal small-subunit (SSU) ribosomal DNA (rDNA) primer set and 16S rDNA primer sets specifically targeting type I methylotrophs (members of the gamma subdivision of the class Proteobacteria [gamma-Proteobacteria]) and type II methylotrophs (members of the alpha-Proteobacteria) were used. Functional PCR primers targeted the genes for particulate methane monooxygenase (pmoA) and methanol dehydrogenase (mxaF), which code for key enzymes in the catabolism of all methanotrophs. The yield of PCR products amplified from DNA in soil that oxidized CH4 was the same as the yield of PCR products amplified from control soil when the universal SSU rDNA primer set was used but was significantly greater when primer sets specific for methanotrophs were used. The DGGE patterns and the sequences of major DGGE bands obtained with the universal SSU rDNA primer set showed that the community structure was dominated by nonmethanotrophic populations related to the genera Flavobacterium and Bacillus and was not influenced by CH4. The structure of the methylotroph community as determined with the specific primer sets was less complex; this community consisted of both type I and type II methanotrophs related to the genera Methylobacter, Methylococcus, and Methylocystis. DGGE profiles of PCR products amplified with functional gene primer sets that targeted the mxaF and pmoA genes revealed that there were pronounced community shifts when CH4 oxidation began. High CH4 concentrations stimulated both type I and II methanotrophs in rice field soil with a nonsaturated water content, as determined with both ribosomal and functional gene markers.

Journal Article↗
PubMed2003

Global functional profiling of gene expression.

The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independent of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function, and chromosome location. Statistical significance values are calculated for each category. We demonstrate the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer datasets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms.

Breast Neoplasms↗
PubMed1997

Conserved clusters of functionally related genes in two bacterial genomes.

An approach for genome comparison, combining function classification of gene products and sequence comparison, is presented. The genomes of Haemophilus influenzae and Escherichia coli are analyzed, and all genes are classified into nine major functional classes, corresponding to important cellular processes. To study gene order relationships and genome organization in the two bacteria, we performed statistics on neighboring pairs of genes. To estimate the significance of the observations, a statistical model based on binomial distributions has been developed. Significant patterns of gene order are observed within, as well as between, the two bacterial genomes: Functionally related genes tend to be neighbors more often than do unrelated genes. Some of these groups represent well-known operons, but additional gene clusters are identified. These clusters correspond to genomic elements that have been conserved during bacterial evolution. In addition to nearest-neighbor relationships, the method is also useful to study the relative direction of transcription in genomes, which is also highly conserved between homologous gene pairs. This new approach combines the high-level description of molecular function with pair statistics that express genome organization. It is expected to complement traditional methods of sequence analysis in the study of genomic structure, function, and evolution.

Binomial Distribution↗
PubMed1995

Identification of a second region upstream of the mouse heme oxygenase-1 gene that functions as a basal level and inducer-dependent transcription enhancer.

A 161-base pair fragment (AB1) approximately 10 kilobase pairs upstream of the transcription start site of the mouse heme oxygenase-1 gene functions as a basal level and inducer-dependent enhancer. AB1/chloramphenicol acetyltransferase fusion genes stably transfected into mouse hepatoma (Hepa) cells or L929 fibroblasts were activated 7-8- or 17-22-fold, respectively, after treatment of the cells with either CdCl2 or heme. The AB1 fragment is composed largely of three tandem repeats containing two conserved core elements, A and B. Part of core element A (TCCGGAGCTGTG) resembles the consensus-binding site for transcription factor AP-4, whereas core element B (GCTGAGTCANGG) includes the consensus-binding site (TGAGTCA) for the AP-1 family of transcription factors. Nuclear proteins from Hepa cells did not bind to any of the core A elements, but bound to all three copies of the core B element. AB1 derivatives with one or two mutant AP-1-binding elements exhibited reduced but measurable inducer-dependent enhancer activity, but mutation of all three AP-1-binding sites abolished activation by CdCl2 and heme and also by mercury chloride, zinc chloride, H2O2, sodium arsenate, and 12-O-tetradecanoylphorbol-13-acetate. Pretreatment of stably transfected L929 cells with protein kinase C inhibitors, but not with tyrosine kinase inhibitors or N-acetylcysteine, abrogated 12-O-tetradecanoylphorbol-13-acetate-dependent activation of the AB1/chloramphenicol acetyltransferase fusion gene. Induction by H2O2 was unaffected by the kinase inhibitors, but completely abolished by N-acetylcysteine. Heme-dependent induction was not significantly affected by any of these chemicals.

Acetylcysteine↗
PubMed1995

Regulation of the Caulobacter crescentus rpoN gene and function of the purified sigma 54 in flagellar gene transcription.

The sequential transcription of flagellar (fla) genes in the Caulobacter crescentus cell cycle is controlled by the organization of these genes in a regulatory hierarchy of four levels (I-IV). Level III and level IV genes at the bottom of the hierarchy are dependent on level II genes and are transcribed late in the cell cycle from sigma 54-dependent promoters. To study the regulation of genes at levels III and IV, we have isolated and sequenced the rpoN gene in order to analyze its expression, purified the rpoN gene product, and examined the role of the RpoN protein in initiation of transcription from sigma 54-dependent promoters. We report here epistasis experiments that show rpoN is required for transcription of level III genes, but that the expression of the rpoN gene itself is not dependent on any of the fla genes examined; these results place rpoN at level II near the top of the hierarchy. Consistent with this conclusion were nuclease S1 assays that mapped the rpoN transcription start site and identified a sequence centered at -24, GTTA/TACCA/TT, which is similar to the core consensus sequence of the level IIB fliF, fliL, and fliQ promoters. We purified the full-length rpoN gene product to near homogeneity and demonstrated that the RpoN protein is required for transcription from the well-characterized sigma 54-dependent glnAp2 promoter of Escherichia coli and specifically recognizes the level III flbG gene promoter of C. crescentus. These last results confirm that rpoN encodes the C. crescentus sigma 54 factor and opens the way for the biochemical analysis of transcriptional regulation of level III and IV fla genes.

Amino Acid Sequence↗
PubMed1987

Structure and expression of HLA-DQ alpha and -DX alpha genes: interallelic alternate splicing of the HLA-DQ alpha gene and functional splicing of the HLA-DQ alpha gene using a retroviral vector.

The nucleotide sequences of the two closely related HLA-DQ alpha and HLA-DX alpha genes have been determined. Exons coding for the signal peptide, alpha 2 and transmembrane domains are 94-99% homologous, whereas the alpha 1 exon and the promoter region have diverged as much as or more than introns and the 3' untranslated region. The promoter regions of both genes contain two short sequences thought to be important for regulation of transcription by gamma-interferon. Transfection studies established that the DQ alpha and DQ beta genes encode the HLA-DQ antigen. Transcripts of varying length are produced from different alleles as the result of the use of alternate splice and polyadenylation signals at the 3' end of the DQ alpha gene. Thus typing at the DQ alpha locus can be achieved by Northern blot analysis. No transcript of DX alpha was detected in B lymphocytes. The DX alpha gene was accurately spliced when introduced into a retroviral vector, suggesting that the lack of expression of DX alpha is not due to aberrant splice signals.

Alleles↗
PubMed1997

A sequence conserved in vertebrate Hox gene introns functions as an enhancer regulated by posterior homeotic genes in Drosophila imaginal discs.

The intron of the mouse Hoxa-4 gene acts as a strong homeotic response element in Drosophila melanogaster leg imaginal discs. This activity depends on homeodomain binding sites present within a 30 bp conserved element, HB1, in the intron. A similar arrangement of homeodomain binding sites is found in many other potential homeotic target genes. HB1 activity in Drosophila imaginal discs is activated by Antennapedia and more posterior homeotic genes, but is not activated by more anterior genes. Testing a reporter gene construct with mutated binding sites in mouse embryos shows that HB1 is also active in the expression domains of posterior Hox genes in the mouse neural tube.

Animals↗
PubMed1989

Human thymidylate synthase gene: isolation of phage clones which cover a functionally active gene and structural analysis of the region upstream from the translation initiation codon.

Two genomic DNA fragments partially encoding human thymidylate synthase (TS) [EC 2.1.1.45] were previously cloned in lambda phage from the mouse cell transformant, but had no transforming activity on mouse TS-negative mutant cells. In this study, an additional genomic DNA for human TS was cloned and demonstrated to have the transforming activity in combination with one of the two previously cloned DNAs and to produce human TS mRNA. The two transforming genomic DNAs overlapped and covered a region of 23 kb in total. Using fragments from one of these DNAs, the structure of the 1.2-kb region around the ATG initiator codon of the TS gene was analyzed in relation to regulatory sequences of the gene. Sequence determination demonstrated the presence of an unusual inverted repeat consisting of a triple tandem repeat of a 28-bp sequence and an inverted sequence of the same length. These sequences can form three possible, stable, stem-loop structures, which may be interconvertible. Based on S1 nuclease mapping data and a line of circumstantial evidence, we deduced two major mRNA cap sites within the inverted sequence. Comparison of the human and mouse sequences upstream from the ATG initiator codon revealed many significant blocks of sequence homology, especially in the regions around the deduced cap sites.

Animals↗
PubMed1997

Adenoviral transfection of isolated pancreatic islets: a study of programmed cell death (apoptosis) and islet function.

Gene therapy provides a potential technique to modify immunity in vitro and therefore may prolong graft survival in vivo. However, viral infection and gene transfer may damage target cells and interfere with biologic function. Viruses, including adenovirus, are known to be capable of modulating apoptosis and initiating cell death by either inducing or suppressing specific processes, depending on the virus and cell system studied. The effect of adenovirus on islet cell viability and function has not been examined in detail. In this study, the dose-dependent effect of an adenoviral vector on islet cell death and glucose-stimulated insulin secretion (GSIS) was investigated to establish a therapeutic window for the dose of viral vector administered. Isolated pancreatic rat islets were incubated with an adenovirus expressing a beta-galactosidase gene (AdHCMVsp1LacZ) at different viral concentrations [multiplicity of infection (MOI) 1:10, 1:100, and 1:1000]. Transfection rate, in vitro and in vivo islet viability, and occurrence of programmed cell death were determined 1, 3, and 7 days after transfection. Islets, transfected at MOI 1:10 and 1:100, demonstrated apoptosis not significantly different from nontransfected controls. Islets, transfected at MOI 1:1000, demonstrated a significant increase in apoptosis at 24 hr, which decreased over 7 days of culture. The increase in apoptosis was not reflected by a significant decrease in in vitro GSIS of surviving islet cells, as assessed by stimulation index following in vitro perifusion. SCID or nude mice transplanted with AdlacZ-transfected islets (MOI 1:100 and 1:1000) remained normoglycemic for > or = 30 days. These results demonstrate that transfection of islets using adenoviral vectors can be manipulated such that efficient expression of the gene product encoded by the transfected gene (beta-galactosidase) can be achieved at lower transfecting concentrations of the adenoviral vector (MOI 1:10, 20.2%; MOI 1:100, 30.7%) while preserving islet function. This efficiency of transfection may allow pretransplant manipulation of isolated islet cells without vector-specific alteration of islet function. In cases where high virus concentrations are required for efficient gene transfer (adequate expression of the transgene product), a deleterious effect of the vector on islet cell function, with increased cell loss due to increased apoptotic events, is predicted. Using the AdlacZ vector, cell loss by apoptotic mechanisms appears limited to the first days following coculture with high viral concentrations, and does not appear to influence in vitro or in vivo cell function of the surviving islet cells.

Adenoviridae↗
PubMed1998

Positive Darwinian selection after gene duplication in primate ribonuclease genes.

Evolutionary mechanisms of origins of new gene function have been a subject of long-standing debate. Here we report a convincing case in which positive Darwinian selection operated at the molecular level during the evolution of novel function by gene duplication. The genes for eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) in primates belong to the ribonuclease gene family, and the ECP gene, whose product has an anti-pathogen function not displayed by EDN, was generated by duplication of the EDN gene about 31 million years ago. Using inferred nucleotide sequences of ancestral organisms, we showed that the rate of nonsynonymous nucleotide substitution was significantly higher than that of synonymous substitution for the ECP gene. This strongly suggests that positive Darwinian selection operated in the early stage of evolution of the ECP gene. It was also found that the number of arginine residues increased substantially in a short period of evolutionary time after gene duplication, and these amino acid changes probably produced the novel anti-pathogen function of ECP.

Amino Acid Sequence↗
PubMed2003

Pigmentary switches in domestic animal species.

Although homogeneous pigmentation usually is observed in wild animals, most domestic animal species display a wide variety of coat colors. In fur animals, the coat color is an important production trait, and in other species such as cattle and sheep, the coat color is a major breed characteristic. Variability in coat color is seen both within and between breeds, and makes domesticated species unique for studying gene function and gene regulation of loci affecting pigmentation. In several species, mutations in the MC1-R gene have been shown to cause the dominant expression of black pigment. In fox, alleles of both the agouti and the MC1-R gene could cause eumelanin synthesis. In addition, a nonepistatic interaction between MC1-R and agouti has been observed, resulting in several different coat color phenotypes expressing a mixture of red and black pigmentation. Also in cattle and sheep, amino acid substitutions within the MC1-R explain the dominant inheritance of black pigmentation. Unlike the constitutively activated MC1-R found in the Alaska silver fox, dominant variants of the MC1-R found in cattle and sheep seem to be completely dominant with no antagonizing effect of agouti. MC1-R variants with premature stop codons are widespread in several cattle populations, indicating that this well-conserved gene has no other fundamental function beside pigmentation. Other well-established breed characteristics include distinct coat color patterns in which the distribution of melanocytes, partly regulated by the c-kit gene, seems to be involved.

Alleles↗