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At least 559 records · Page 31Linked to original sources
PubMed1999

G proteins, chemosensory perception, and the C. elegans genome project: An attractive story.

Heterotrimeric G proteins, consisting of alpha, beta, and gamma subunits, couple ligand-bound seven transmembrane domain receptors to the regulation of effector proteins and production of intracellular second messengers. G protein signaling mediates the perception of environmental cues in all higher eukaryotic organisms, including yeast, Dictyostelium, plants, and animals. The nematode Caenorhabditis elegans is the first animal to have complete descriptions of its cellular anatomy, cell lineage, neuronal wiring diagram, and genomic sequence. In a recent paper, Jansen et al. used sequence searches of the C. elegans genome database to identify all heterotrimeric G protein genes (20 Galpha, 2 Gbeta, 2 Ggamma). C. elegans encodes one ortholog of each of the four Galpha classes found in metazoans and 16 new Galpha genes. The orthologous genes are widely expressed, whereas 14 of the divergent Galpha genes are almost exclusively expressed in sensory neurons where they may regulate perception and chemotaxis.

Animals↗
PubMed1989

Comparison of the gap segmentation gene hunchback between Drosophila melanogaster and Drosophila virilis reveals novel modes of evolutionary change.

We have cloned and sequenced a large portion of the hunchback (hb) locus from Drosophila virilis. Comparison with the Drosophila melanogaster hb sequence shows multiple strong homologies in the upstream and downstream regions of the gene, including most of the known functional parts. The coding sequence is highly conserved within the presumptive DNA-binding finger regions, but more diverged outside of them. The regions of high divergence are correlated with regions which are rich in short direct repeats (regions of high 'cryptic simplicity'), suggesting a significant influence of slippage-like mechanisms in the evolutionary divergence of the two genes. Staining of early D.virilis embryos with an hb antibody reveals conserved and divergent features of the spatial expression pattern at blastoderm stage. It appears that the basic expression pattern, which serves as the gap gene function of hb, is conserved, while certain secondary expression patterns, which have separate functions for the segmentation process, are partly diverged. Thus, both slippage driven mutations in the coding region, which are likely to occur at higher rates than point mutations and the evolutionary divergence of secondary expression patterns may contribute to the evolution of regulatory genes.

Amino Acid Sequence↗
PubMed2000

Genetic control of regional identity in the developing vertebrate forebrain.

In the past we isolated and characterized a number of vertebrate homeobox genes expressed in the developing brain. In particular, Emx1 and Emx2 are expressed in the developing forebrain of mouse embryos, in a region including the presumptive cerebral cortex. In the developing cerebral cortex, Emx1 is expressed in most neuroblasts and neurons at all stages of development, whereas Exm2 expression is restricted to proliferating neuroblasts of the so-called ventricular zone and to Cajal-Retzius cells, but is undetectable in most postmitotic cortical neurons. It is conceivable to hypothesize that Emx2 plays a role in the control of proliferation of cortical neuroblasts and in the regulation of their subsequent migration. This latter process has been recently analysed in some detail in null mutant mice. The expression of these and other genes has also been analysed in the developing brain of different species of vertebrates. Homologies between forebrain subdivisions have been proposed based on the conservation and divergence of gene expression patterns.

Animals↗
PubMedDate not supplied

Analysis of a repeat-containing family of Giardia lamblia variant-specific surface protein genes: diversity through gene duplication and divergence.

Giardia lamblia trophozoites express on their surfaces one of a set of cysteine-rich antigenically variant proteins, called variant-specific surface proteins, which comprise the majority of proteins detected by surface labeling. While these VSP proteins may be immunodominant proteins important in the host immune response to G. lamblia, the ability to switch expression from one VSP to another may provide a means for the trophozoites to avoid the host immune response. The first VSP characterized, VSPA6 (from the A6 clone of the WB isolate, originally termed CRP170), contains 18-23 copies of a 65 amino acid repeat. We have now used the repeat as a probe to isolate from a WBA6 genomic library two genes related to vspA6 (called vspA6-S1, vspA6-S2). Sequence analysis of the vspA6-S1 gene revealed nearly two complete copies of the 195 bp repeat and substantial nucleotide and translated amino acid similarity in the coding regions 5' and 3' to the repeats. The vspA6-S2 gene, while still related, showed greater divergence from vspA6 than vspA6-S1 in the nonrepeat coding region and contained nearly four copies of a 201 bp repeat that was 75% identical to the 195 bp vspA6 repeat. These results suggest that gene duplication followed by divergence has played a key role in the generation of the vsp gene repertoire.

Amino Acid Sequence↗
PubMed1990

Bidirectional promoter activity of the 5' flanking region of the mouse thymidine kinase gene.

The 5' flanking region of the gene coding for cytoplasmic thymidine kinase (TK) in the mouse (a total of 490 bp upstream of the initiation codon) was tested for promoter activity using the chloramphenicol acetyltransferase gene as reporter. It was found that the region can be divided into two parts, one of which carries promoter activity in the direction of TK, whereas the 5'-half has promoter activity in the opposite direction. A fragment of 140 bp was sufficient for growth-dependent promoter activity in the direction of TK, although about 100 bp further upstream, enhanced the activity. Expression from the divergent promoter was independent of cell growth.

Animals↗
PubMed1989

Chromosomal location and evolutionary rate variation in enterobacterial genes.

The basal rate of DNA sequence evolution in enterobacteria, as seen in the extent of divergence between Escherichia coli and Salmonella typhimurium, varies greatly among genes, even when only "silent" sites are considered. The degree of divergence is clearly related to the level of gene expression, reflecting constraints on synonymous codon choice. However, where this constraint is weak, among genes not expressed at high levels, divergence is also related to the chromosomal location of the gene; it appears that genes furthest away from oriC, the origin of replication, have a mutation rate approximately two times that of genes near oriC.

Bias↗
PubMed2006

Gender differences in renal nuclear receptors and aryl hydrocarbon receptor in 5/6 nephrectomized rats.

This study was aimed at delineating molecular pathways essential in gender-different pathogenesis of chronic kidney diseases (CKD). Renal transcripts of nuclear receptors and metabolic enzymes in male and female kidneys from 5/6 nephrectomized (Nx) rats 7 weeks post-Nx were examined using branched DNA signal amplification assay. Nx-males had marked kidney injury coupled with anemia and malnutrition. Nx-females had moderate renal injury, and were free of albuminuria, anemia, and malnutrition. Nx-males had systemic and renal inflammation, which were largely absent in Nx-females. Blood 17beta-estradiol, testosterone, and corticosterone did not change, whereas urinary testosterone decreased in both genders. Compared to males, female kidneys had higher androgen receptor (AR) and aryl hydrocarbon receptor (AhR) but lower estrogen receptor alpha (ERalpha). Compared to Nx-males, female remnant kidneys had less decreases in ERalpha and peroxisome proliferator-activated receptor alpha (PPARalpha), had no induction of AR and decrease of acyl-CoA oxidase, whereas had induction of cytochrome P450 4a1 (Cyp4a1) but decrease of AhR. Renal protein expression of a 52-kDa isoform of Wilm's tumor 1 (WT1), transcription factor critical in nephrogenesis, decreased dramatically in Nx-males but largely preserved in Nx-females. In conclusion, gender divergences in basal expression and alteration of ERalpha, AR, AhR, WT1, and PPARalpha/Cyp4a1 during CKD may explain gender differences in CKD progression and outcome of renal transplantation.

Acyl-CoA Oxidase↗
PubMed2002

Specificity of the cyclic adenosine 3',5'-monophosphate signal in granulosa cell function.

Cyclic AMP signaling is involved in most aspects of differentiation and maturation of the granulosa cells in the ovarian follicle. As the genetic programs activated at different stages of follicle growth maturation are being elucidated, it is becoming increasingly difficult to reconcile the simplicity of the cAMP cascade with the complexity and the divergent patterns of gene expression activated in these cells. To account for these divergent outcomes of the cAMP signal, three aspects of this signaling cascade in granulosa cells will be reviewed. We will discuss the evidence for gonadotropin receptors coupling to different G proteins and effectors. Next, we will explore the possibility that the temporal and spatial dimensions of the cAMP signal itself may contribute to the diverse outcomes. Finally, we will summarize available data showing that the cAMP signal is distributed through several cascades of kinase activation. It is hoped this compendium will provide a framework with which to understand how the initial signals activated by gonadotropins control the complex patterns of gene expression that are required for follicle maturation and ovulation.

Adenylyl Cyclases↗
PubMed1998

Tomato fructokinases exhibit differential expression and substrate regulation

Two divergent genes encoding fructokinase, Frk1 and Frk2, have been previously shown to be expressed in tomato (Lycopersicon esculentum L.) and have now been further characterized with regard to their spatial expression and the enzymic properties of the encoded proteins. Frk1 and Frk2 mRNA levels were coordinately induced by exogenous sugar, indicating that both belong to the growing class of sugar-regulated genes. However, in situ hybridization indicated that Frk1 and Frk2 were expressed in a spatially distinct manner, with Frk2 mRNA primarily localized in cells of the fruit pericarp, which store starch, and Frk1 mRNA distributed ubiquitously in pericarp tissue. To evaluate the biochemical characteristics of the products of the Frk1 and Frk2 genes, each cDNA was expressed in a mutant yeast (Saccharomyces cerevisiae) line defective in hexose phosphorylation and unable to grow on glucose or fructose (Fru). Both Frk1 and Frk2 proteins expressed in yeast conferred the ability to grow on Fru and exhibited fructokinase activity in vitro. Although both Frk1 and Frk2 both utilized Fru as a substrate, only Frk2 activity was inhibited at high Fru concentrations. These results indicate that Frk2 can be distinguished from Frk1 by its sensitivity to substrate inhibition and by its temporal and spatial pattern of expression, which suggests that it plays a primary role in plant cells specialized for starch storage.

Journal Article↗
PubMed1999

Prognostic significance of Bcl-2 in Wilms' tumor and oncogenic potential of Bcl-X(L) in rare tumor cases.

Anaplastic Wilms' tumors are commonly believed to be rare forms of progression, driven by p53 mutations, of the more common classical Wilms' tumor or nephroblastoma Contrary to classical Wilms' tumors, anaplastic tumors traditionally tend to metastasize, to be drug-resistant and to have a poor prognosis. The Bcl-2 gene product protects cells from programmed cell death, and its over-expression has been proposed to be tumorigenic and to mediate resistance to therapy. Because Bcl-2 has been reported to be transcriptionally repressed by p53, using immuno-histochemistry and mRNA analyses, we have examined Bcl-2 expression in a panel of 10 classical and 3 anaplastic nephroblastomas in which the p53 status had been previously analyzed. We found that classical Wilms' tumors expressed significant amounts of Bcl-2 mRNA and protein, whereas anaplastic tumors did not, regardless of p53 mutations. However, because mortality occurred both among patients with classical and among those with anaplastic tumors, which had divergent Bcl-2 expression, analysis of variance failed to demonstrate prognostic Bcl-2 significance. Therefore, we examined the expression of the Bcl-X and Bax genes, which are known to synergize and antagonize Bcl-2, respectively. With the exception of anaplastic tumor W17, the monotony of Bcl-X and Bax mRNA levels did not suggest that the expression of these apoptosis-regulating genes could have a role in the prognosis of nephroblastoma. In addition to the standard 2.7-kb Bcl-X(L) mRNA, W17 expressed a 3.5-kb mRNA species which had the same coding capacity for Bcl-X(L) as the 2.7-kb mRNA. Western analysis demonstrated that W17 had the highest level of Bcl-X(L) protein, suggesting that Bcl-X(L) over-expression could play a part in the development of anaplasia in rare Wilms' tumor cases without affecting prognosis.

Blotting, Northern↗
PubMed2006

Simian varicella virus gene 28 and 29 promoters share a common upstream stimulatory factor-binding site and are induced by IE62 transactivation.

Simian varicella virus (SVV) is a neurotropic alphaherpesvirus that causes a natural, varicella-like disease in non-human primates. After resolution of the primary disease, SVV, like its human counterpart, varicella-zoster virus (VZV), establishes latent infection in the neural ganglia of the host. In this study, gene expression of SVV open reading frames (ORFs) 28 and 29, which encode the viral DNA polymerase and DNA-binding protein, respectively, was characterized during lytic infection of Vero cells. The results indicate that the intergenic region controlling gene 28 and 29 expression includes overlapping, divergent promoters. The ORF 28 and 29 promoters are active in SVV-infected Vero cells, but not in uninfected cells. The SVV immediate-early gene 62 (IE62) product transactivates ORF 28 and 29 expression, and a cellular upstream stimulatory factor-binding site is important for efficient IE62 induction of genes 28 and 29. DNA sequence analysis of the 185 bp intergenic region identified putative cellular transcription factor-binding sites. Transcriptional analysis mapped ORF 28 and 29 RNA start sites. A recombinant SVV was employed to demonstrate that the ORF 29 promoter can express a heterologous gene (green fluorescent protein) when inserted into a novel site (the ORF 12/13 intergenic region) within the SVV genome. The findings demonstrate similarities between SVV and VZV ORF 28/29 expression and indicate that the simian varicella model may be useful to investigate the differential regulation of viral genes during lytic and latent infection.

Amino Acid Sequence↗
PubMed2001

Petunia Ap2-like genes and their role in flower and seed development.

We have isolated three Apetala2 (Ap2)-like genes from petunia and studied their expression patterns by in situ hybridization. PhAp2A has a high sequence similarity to the A function gene Ap2 from Arabidopsis and a similar expression pattern during flower development, suggesting that they are cognate orthologs. PhAp2B and PhAp2C encode for AP2-like proteins that belong to a different subgroup of the AP2 family of transcription factors and exhibit divergent, nearly complementary expression patterns during flower development compared with PhAp2A. In contrast, all three PhAp2 genes are strongly expressed in endosperm. The phenotype of the petunia A-type mutant blind cannot be attributed to mutations in the petunia Ap2 homologs identified in this study, and reverse genetics strategies applied to identify phap2a mutants indicate that PhAp2A might not be essential for normal perianth development in petunia. Nevertheless, we show that PhAp2A is capable of restoring the homeotic transformations observed in flowers and seed of the ap2-1 mutant of Arabidopsis. Although the interspecific complementation proves that PhAp2A encodes a genuine Ap2 ortholog from petunia, additional factors may be involved in the control of perianth identity in this species.

Amino Acid Sequence↗
PubMed2000

A single naturally processed measles virus peptide fully dominates the HLA-A*0201-associated peptide display and is mutated at its anchor position in persistent viral strains.

We studied the natural MHC class I display of measles virus (MV) epitopes. Peptide ligands associated with HLA-A*0201 were purified from a B lymphoblastoid cell line prior to and after infection with MV. Infection-induced peptides were revealed using microcapillary reversed phase high performance liquid chromatography electrospray ionization/mass spectrometry (microLC-ESI/MS) by subtraction of the "infected" and "uninfected" ion traces. Three naturally processed viral epitopes derived from different MV proteins were identified through tandem MS sequencing. These peptides were expressed at widely divergent levels of HLA-peptide complexes, but had similar binding capacities to HLA-A*0201. The most abundant viral peptide species, identified as residues 84-92 (KLWESPQEI) of the MV nonstructural C protein, was expressed at an unprecedented high density (> 10(5) copies per cell) and was immunogenic in HLA-A2/Kb-transgenic mice. Furthermore, natural mutants of this epitope, occurring in persistent lethal MV strains, were shown to have lost their HLA-A*0201 binding capacity. Thus, here we report for the first time the direct discovery through microLC-ESI/MS of a uniquely dominant viral HLA class I ligand, KLWESPQEI, with features eligible for immune selection pressure.

Amino Acid Sequence↗
PubMed2006

Expression of otd orthologs in the amphipod crustacean, Parhyale hawaiensis.

The arthropod head is a complex metameric structure. In insects, orthodenticle (otd) functions as a 'head gap gene' and plays a significant role in patterning and development of the anterior head ectoderm, the protocerebrum, and the ventral midline. In this study, we characterize the structure and developmental deployment of two otd paralogs in the amphipod crustacean, Parhyale hawaiensis. Photd1 is initially expressed at gastrulation through germband stages in a bilaterally symmetric, restricted region of the anterior head ectoderm and also in a single column of cells along the ventral midline. Late in embryogenesis, Photd1 is expressed within the developing anterior brain and the expression along the embryonic midline has become restricted to a stereotypic group of segmentally reiterated cells. The second ortholog Photd2, however, has a unique temporal-spatial expression pattern and is not detected until after the head lobes have been organized in the developing ectoderm of the germband during late germband stages. Anteriorly, Photd2 is coincident with the Photd1 head expression domain; however, Photd2 is not detected along the ventral midline during formation of the germband and only appears in the ventral midline late in embryonic development in a restricted group of cells distinct from those expressing Photd1. The early expression of Photd1 in the anterior head ectoderm is consistent with a role as a head gap gene. The more posterior expression of Photd1 is suggestive of a role in patterning the embryonic ventral midline. Photd2 expression appears too late to play a role in early head patterning but may contribute to latter patterning in restricted regions of both the head and the ventral midline. The comparative analysis of otd reveals the divergence of gene expression and gene function associated with duplication of this important developmental gene.

Animals↗
PubMed2003

Regulation of p21 and p27 expression by the hepatitis B virus X protein and the alternate initiation site X proteins, AUG2 and AUG3.

BACKGROUND: The hepatitis B virus X gene has three in-frame start codons encoding the pX, AUG2 and AUG3 proteins. The AUG2 and AUG3 genes are 5'-truncated in respect to the full-length pX gene; however, all three genes terminate at the same stop codon. The activity of pX as an oncogene is well characterized; however, less is known about the AUG2 and AUG3 proteins. METHODS: The effects of pX, AUG2 and AUG3 on p21Cip,1/WAF,1/MDA6 and p27Kip-1 cyclin kinase inhibitor (CKI) protein expression, and the impact they have on proliferation, were investigated in CHO K-1 cells. CHO K-1 cells were chosen because they can be transfected at 100% efficiency. RESULTS: p21- and p27-luciferase reporter expression is modulated by increasing doses of the hepatitis B X proteins. At low concentrations of pX or AUG2, p21- and p27-luciferase activity was increased, and at high concentrations, p21- and p27-luciferase activity was decreased. Expression of the AUG3 gene showed a different profile: it was increasingly stimulatory with dose for both promoters. Western blot analyses demonstrated that p21 and p27 protein levels were modulated as predicted based on data generated in the promoter-luciferase experiments. Tritiated thymidine labeling of DNA showed biphasic kinetics of incorporation in the presence of varying pX and AUG2 concentrations, whereas labeling decreased with AUG3 concentration. The growth inhibitory effect of pX expression was reduced by antisense ablation of either p21 or p27. CONCLUSIONS: The relative expression level of pX, AUG2, and AUG3 impacts on CKI expression and cell proliferation. Our findings may explain why divergent effects of pX expression on growth have been observed by different groups, which may be related to relative pX expression levels.

Animals↗
PubMed2005

Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program.

Differences in gene expression underlie many of the phenotypic variations between related organisms, yet approaches to characterize such differences on a genome-wide scale are not well developed. Here, we introduce the "differential clustering algorithm" for revealing conserved and diverged co-expression patterns. Our approach is applied at different levels of organization, ranging from pair-wise correlations within specific groups of functionally linked genes, to higher-order correlations between such groups. Using the differential clustering algorithm, we systematically compared the transcription program of the fungal pathogen Candida albicans with that of the model organism Saccharomyces cerevisiae. Many of the identified differences are related to the differential requirement for mitochondrial function in the two yeasts. Distinct regulation patterns of cell cycle genes and of amino acid metabolic genes were also revealed and, in some cases, could be linked to the differential appearance of cis-regulatory elements in the gene promoter regions. Our study provides a comprehensive framework for comparative gene expression analysis and a rich source of hypotheses for uncharacterized open reading frames and putative cis-regulatory elements in C. albicans.

Candida albicans↗
PubMed2006

Deletion of RNQ1 gene reveals novel functional relationship between divergently transcribed Bik1p/CLIP-170 and Sfi1p in spindle pole body separation.

Spindle pole body (SPB; the microtubule organizing center in yeast) duplication is essential to form a bipolar spindle. The duplicated SPBs must then separate and migrate to opposite sides of the nucleus. We identified a novel functional relationship in SPB separation between the microtubule stabilizing protein Bik1p/CLIP-170 and the SPB half-bridge protein Sfi1p. A genetic interaction between BIK1 and SFI1 was discovered in a synthetic lethal screen using a strain deficient in the prion protein gene RNQ1. RNQ1 deletion reduced expression from the divergently transcribed BIK1, allowing us to identify genetic interactors with bik1. The sfi1-1 bik1 synthetic lethality was suppressed by over-expression of CIK1, KAR1, and PPH21. Genetic analysis indicated that the sfi1-1 bik1 synthetic lethality was unlikely related to the function of Bik1p in the dynein pathway or to defects in spindle position. Furthermore, a sfi1-1 Deltakip2 mutant was viable, suggesting that the Bik1p pool at the cytoplasmic microtubule plus-ends may not be required in sfi1-1. Microscopic examination indicated the sfi1-1 mutant was delayed in SPB duplication, SPB separation, or spindle elongation and the sfi-1 Deltabik1 double mutant arrested with duplicated but unseparated SPBs. These results suggest that Bik1p has a previously uncharacterized function in the separation of duplicated SPBs.

Alleles↗
PubMed1994

Differential expression and activation of a family of murine peroxisome proliferator-activated receptors.

To gain insight into the function of peroxisome proliferator-activated receptor (PPAR) isoforms in mammals, we have cloned and characterized two PPAR alpha-related cDNAs (designated PPAR gamma and -delta, respectively) from mouse. The three PPAR isoforms display widely divergent patterns of expression during embryogenesis and in the adult. Surprisingly, PPAR gamma and -delta are not activated by pirinixic acid (Wy 14,643), a potent peroxisome proliferator and activator of PPAR alpha. However, PPAR gamma and -delta are activated by the structurally distinct peroxisome proliferator LY-171883 and linoleic acid, respectively, indicating that each of the isoforms can act as a regulated activator of transcription. These data suggest that tissue-specific responsiveness to peroxisome proliferators, including certain fatty acids, is in part a consequence of differential expression of multiple, pharmacologically distinct PPAR isoforms.

Acetophenones↗