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At least 397 records · Page 22Linked to original sources
PubMed2006

The Arabidopsis anaphase promoting complex (APC): regulation through subunit availability in plant tissues.

Sister-chromatid separation and exit from mitosis require ubiquitin-mediated proteolysis of cell cycle regulators such as cyclin B and securin. The specificity of the reaction is controlled by an ubiquitin-ligase multiprotein complex known as APC (Anaphase Promoting Complex). Comparison of the coding sequences of Arabidopsis genes with the Genbank database reveals extensive homology of the predicted ORFs with the corresponding proteins of other eukaryotes, indicating that the APC is well conserved in plants. However, different from other eukaryotes, the Arabidopsis genes have some particular characteristics, such as the presence of two copies of the CDC27 gene. Furthermore, expression analyses of the AtAPC genes disclose complex profiles that differ, depending on the tissue examined. In actively dividing cell suspensions there is a direct correspondence between the rates of proliferation and mRNA levels from the AtAPC components. On the other hand, in plant organs, dark-grown seedlings and during leaf growth, this correlation is lost and the AtAPC genes are highly expressed in tissues with low overall cell division. Moreover, expression patterns diverge between the subunit genes, raising the possibility that there could be more than one form of the APC, which would execute distinct functions during plant development. The results suggest that an important layer of regulation of APC/C in plants could operate through subunit availability in specific tissues and/or cellular compartments.

Amino Acid Sequence↗
PubMed1986

Sequence and expression of the chicken beta 5- and beta 4-tubulin genes define a pair of divergent beta-tubulins with complementary patterns of expression.

We have determined the nucleotide sequence of the chicken beta 5 (c beta 5)-tubulin gene. The gene displayed the coding structure common to all previously studied vertebrate beta-tubulin genes and was divided into four exon sequences interrupted by three intervening sequences (located between codons 19 and 20, within codon 56, and within codon 93). Comparison of the predicted polypeptide sequence encoded by c beta 5 with those of four other available chicken beta-tubulin sequences revealed that c beta 5 encoded a highly divergent beta-tubulin polypeptide isotype which was distinguished from previously known sequences primarily by two discrete variable sequence domains. However, c beta 5 uniquely shared identity in 16 residue positions with another divergent chicken beta-tubulin gene, c beta 4. These common sequences distinguished c beta 4 and c beta 5 from the remaining three chicken beta-tubulin genes. Analysis of the expression of c beta 5 and c beta 4 revealed a strikingly complementary pattern of gene expression: c beta 5 was expressed in a wide variety of cell and tissue types but not in neurons, whereas c beta 4 expression was detected uniquely in neuronal cells. Overall, these findings suggest the existence of two divergent families of beta-tubulin sequences in the chicken and further raise the possibility that the complementary expression of the c beta 4 and c beta 5 genes may fulfill a requirement for the presence of a divergent beta-tubulin polypeptide isotype in all cell types.

Amino Acid Sequence↗
PubMed2004

Methylation and inhibition of expression of uPA by the RAS oncogene: divergence of growth control and invasion in breast cancer cells.

Expression of urokinase-type plasminogen activator (uPA), a protease only expressed in highly invasive human breast cancer cells, is inhibited by DNA methylation of its promoter. We tested the hypothesis that up-regulation of DNA methyltransferase 1 (DNMT1) will lead to methylation and silencing of uPA and inhibition of the invasiveness of metastatic breast cancer cells. Since RAS was previously shown to up-regulate DNA methylation, we examined the effects of ectopic expression of constitutively active RAS on methylation and expression of uPA. Transfection of Ha-RAS into MDA-MB-231 human breast cancer cells resulted in a significantly shorter cell doubling time compared with the controls. However, expression and activity of the metastatic gene uPA and invasive capacity of the cells were significantly reduced by the oncogene RAS. Silencing of uPA by RAS is mediated by a cis modification of the uPA promoter and not through an effect on a trans-acting factor, since a transiently transfected unmethylated uPA-luicferase reporter is expressed at a similar level in RAS-transfected and control cells. We then examined the levels of DNMT1 and methylated DNA-binding protein 2 (MBD2) expressions in these cells to determine whether this reduction in uPA expression is associated with changes in the DNA methylation machinery. Our results showed that ectopic expression of RAS induced DNMT1 expression and activity and inhibited MBD2 expression. Consistent with methylation-mediated repression, uPA was partially methylated in RAS-transfected cells and uPA expression was induced upon treatment of RAS transfectants with the demethylating agent 5'-azacytidine. These results therefore imply that the RAS-DNMT1 DNA methylation pathway which promotes oncogenic growth in many cancers can exert an opposite effect on the invasive capacity of the highly invasive MDA-MB-231 cells, thus illustrating the divergence of growth and metastasis promoting pathways in cancer. This has important implications for new therapeutic approaches to metastasizing cancer.

Base Sequence↗
PubMed1991

Insulin-like growth factor receptor gene expression in the rat ovary: divergent regulation of distinct receptor species.

The intraovarian insulin-like growth factor (IGF) system constitutes a triad composed of ligands, receptors, and binding proteins. Although conventional radioligand receptor assays have documented the presence of specific receptors for insulin and insulin-like peptides in some rat somatic ovarian cell types, the exact cellular localization and hormonal regulation of the receptors in question remain matters of inquiry. To reevaluate the very presence, cellular localization, and hormonal regulation of the IGF receptor gene family in the rat ovary, solution hybridization/RNase protection assays were used wherein ovarian total RNA (20 micrograms) from immature (21-23 days old) rats was hybridized with 32P-labeled type I IGF receptor, type II IGF/mannose-6-phosphate receptor, and insulin receptor riboprobes. Single protected fragments 261 (type I IGF receptor), 500 (type II IGF/mannose-6-phosphate receptor), and 478 (insulin receptor) bases long were evident in whole ovary, granulosa, and theca-interstitial cells. Hypophysectomy of immature rats led to significant (P less than 0.05) albeit variable decrements in the relative (densitometrically quantified) ovarian abundance of transcripts corresponding to the type I IGF (but not insulin or type II IGF/mannose-6-phosphate) receptor. Treatment of immature hypophysectomized rats with FSH (10 micrograms/rat.day x 2.5 days) resulted in a significant (P less than 0.05) increase (4-fold) in transcripts corresponding to the type I IGF receptor in both whole ovarian material and freshly isolated granulosa cells. Similar (3.7-fold) increments (P less than 0.05) were noted after treatment with a diethylstilbestrol-containing sc silastic implant applied for a total of 5 days.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1991

Hepatitis E virus genome. Molecular features, expression of immunoreactive proteins and sequence divergence.

The strategy for molecular cloning of hepatitis E virus (HEV), the major etiologic agent of enterically-transmitted non-A, non-B hepatitis, is briefly described. The organization of the HEV genome is discussed and compared to those of two other vertebrate viruses that contain single-stranded, positive-sense, polyadenylated RNA genomes with three overlapping ORFs. Serologic cross-reactivity of expressed proteins and genetic divergence of HEV isolates are also described within the context of sequence variation, type-common epitopes, and type-specific epitopes.

Cloning, Molecular↗
PubMed2000

Divergent regulation of GAP-43 expression and CNS neurite outgrowth by cyclic AMP.

Robust process outgrowth and high expression of the growth-associated protein GAP-43 seem to be intrinsic features of neurons, but both are down-regulated after axonal contact of target cells. We report that chronic exposure of the serotonergic CNS cell line RN46A to cyclic AMP analogs, forskolin, or cholera toxin represses GAP-43 expression in a dose dependent manner. Thus, cAMP could mediate a GAP-43 repressive signal that is initiated extracellularly. Activation of the cyclic AMP pathway by these same reagents, however, enhances the rate that RN46A cells extend neurites. This stimulation of neurite growth can occur during inhibition of new transcription, and in the absence of high levels of GAP-43. These findings demonstrate that a GAP-43-repressing intracellular signaling pathway exists, that repression of GAP-43 expression by cAMP is not directly coupled to inhibition of neurite growth, and that acceleration of growth cone advancement by cAMP is not dependent on the presence of GAP-43.

1-Methyl-3-isobutylxanthine↗
PubMed2007

Rapid evolution in a pair of recent duplicate segments of rice.

Gene duplication has been considered the most important way of generating genetic novelties. The subsequent evolution right after gene duplication is critical for new function to occur. Here we analyzed the evolutionary pattern for a recently duplicated segment between rice chromosomes 11 and 12. This duplication event was estimated to occur about 6 million years ago, during the divergence of the B- and C-genome rice species. The duplicate segment in chromosome 12 has significantly higher frequency of sequence rearrangement rate than non-duplicated regions. The rearrangement rate is approximately 6.5 breakages/Mb per million years, about six times higher than the fastest rate ever reported in eukaryotes. The genes within both segments experienced accelerated nucleotide substitution rates revealed by synonymous (Ks) and non-synonymous divergence (Ka) between Oryza sativa indica and O. sativa japonica. Analysis using EST data also implicates rapid divergence in expression between these segmental duplicate genes. These overall rapid changes from different perspective for the first time provide evidence that relaxation of selection also occurs in large-scale duplications.

Base Sequence↗
PubMed1998

Arachidonic acid metabolism in the marine fish Stenotomus chrysops (Scup) and the effects of cytochrome P450 1A inducers.

Cytochrome P450-mediated arachidonic acid (AA) metabolism was investigated in the marine fish scup, Stenotomus chrysops. Liver microsomes incubated with AA and NADPH produced epoxyeicosatrienoic acids (EETs) and their hydration products (dihydroxyeicosatrienoic acids, DHETs), midchain conjugated dienols (midchain HETEs), and C16-through C20-alcohols of AA (omega-terminal HETEs), all identified by HPLC and GC/MS. Gravid females had 4-fold lower AA metabolism rates than males but identical metabolite profiles. The 5,6-EET (inferred from stable metabolites) was most abundant (47% of total EETs) followed by 14,15-, 11,12-, and 8,9-EET (27, 13, and 13%, respectively). The 12-HETE represented 25% of total HETEs followed in abundance by 16-, 15-, 11-, 19-, 20-, 8-, and 9-HETE. Antibodies against scup CYP1A and a scup CYP2B-like protein inhibited liver microsomal AA metabolism by 30 and 46%, respectively. GC/MS analysis revealed EETs and DHETs as endogenous constituents in scup liver; the predominant EETs were 8,9- and 14,15-EET, followed by a lesser amount of 11,12-EET. Chiral analysis showed a preference for the S,R-enantiomers of endogenous 8,9-, 11,12-, and 14,15-EET (optical purities 80, 64, and 64%, respectively). Treatment of scup with the CYP1A inducer benzo(a)pyrene (BP) increased liver microsomal formation of EETs and HETEs by 2.7-fold in spring and 1.7-fold in summer. BP treatment did not affect microsomal EET regioselectivity, but shifted hydroxylation in favor of 19-HETE and induced 17-HETE formation. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) treatment in summer did not induce liver microsomal AA metabolism rates, yet BP and TCDD both increased endogenous EET content of liver (5- and 3-fold, respectively), with a shift to 14,15-EET. BP treatment increased the selectivity for the S,R-enantiomers of endogenous 8,9-, 11,12-, and 14,15-EET (optical purities 91, 84, and 83%, respectively). Kidney, gill, and heart microsomes all metabolized AA, at rates 10- to 30-fold less than liver microsomes. Similar amounts of endogenous 8,9- and 14,15-EET and less 11,12-EET were detected in heart and kidney, and there was a strong enantioselectivity for 8(R),9(S)-EET in heart (optical purity 78%) but not in kidney. BP treatment did not alter the total EET content in these organs but did shift the regiochemical profile in heart to favor 14,15-EET. Thus, scup liver and extrahepatic organs metabolize AA via multiple cytochrome P450 (CYP) forms to eicosanoids in vitro and in vivo. BP or TCDD induced endogenous AA metabolism in liver, altering EET regioselectivity and, with BP, stereoselectivity. While AhR agonists alter metabolism of AA in early diverging vertebrates expressing both CYP1A and AhR, the magnitude of effects may depend upon the type of inducer.

12-Hydroxy-5,8,10,14-eicosatetraenoic Acid↗
PubMed2001

Leiomodins: larger members of the tropomodulin (Tmod) gene family.

The 64-kDa autoantigen D1 or 1D, first identified as a potential autoantigen in Graves' disease, is similar to the tropomodulin (Tmod) family of actin filament pointed end-capping proteins. A novel gene with significant similarity to the 64-kDa human autoantigen D1 has been cloned from both humans and mice, and the genomic sequences of both genes have been identified. These genes form a subfamily closely related to the Tmods and are here named the Leiomodins (Lmods). Both Lmod genes display a conserved intron-exon structure, as do three Tmod genes, but the intron-exon structure of the Lmods and the Tmods is divergent. mRNA expression analysis indicates that the gene formerly known as the 64-kDa autoantigen D1 is most highly expressed in a variety of human tissues that contain smooth muscle, earning it the name smooth muscle Leiomodin (SM-Lmod; HGMW-approved symbol LMOD1). Transcripts encoding the novel Lmod gene are present exclusively in fetal and adult heart and adult skeletal muscle, and it is here named cardiac Leiomodin (C-Lmod; HGMW-approved symbol LMOD2). Human C-Lmod is located near the hypertrophic cardiomyopathy locus CMH6 on human chromosome 7q3, potentially implicating it in this disease. Our data demonstrate that the Lmods are evolutionarily related and display tissue-specific patterns of expression distinct from, but overlapping with, the expression of Tmod isoforms.

Amino Acid Sequence↗
PubMed2025

Quantitative Real-Time PCR for Circular RNA Detection and Analysis.

In eukaryotes, nearly 2% of the genome represented by the coding proteins. However, emerging evidence suggest more than 75% of the human genome referred to as noncoding part also plays a crucial role in governing major regulatory pathways. Noncoding RNAs can be categorized into several groups, such as microRNAs (miRNAs), small nuclear RNA (snRNAs), small nucleolar RNA (snoRNAs), transfer RNA (tRNA), and circular RNA (circRNAs), which contribute to this regulatory landscape. Circular RNAs (circRNAs) are identified as a new class of regulatory noncoding RNAs with gene regulatory roles by acting as miRNA or RNA binding protein sponges or interacting with proteins. Researchers employ quantitative real-time PCR methods to examine circular RNA expression utilizing divergent primers for identification and quantification.

RNA, Circular↗
PubMed2006

New members of the neurexin superfamily: multiple rodent homologues of the human CASPR5 gene.

Proteins of the Caspr family are involved in cell contacts and communication in the nervous system. We identified and, by in silico reconstruction, compiled three orthologues of the human CASPR5 gene from the mouse genome, four from the rat genome, and one each from the chimpanzee, dog, opossum, and chicken genomes. Obviously, Caspr5 gene duplications have taken place during evolution of the rodent lineage. In the rat, the four paralogues are located in one chromosome arm, Chr 13p. In the mouse, however, the three Caspr5 genes are located in two chromosomes, Chr 1 and Chr 17. RT-PCR shows that all three mouse paralogues are being expressed. Common expression is found in brain tissue but different expression patterns are seen in other organs during fetal development and in the adult stage. Tissue specificity of expression has diverged during evolution of this young rodent gene family.

Animals↗
PubMed2006

Similarity and divergence in the development and expression of the mouse and human antibody repertoires.

Over the past twenty years diverse groups in Northeast Asia, Western Europe, and North America have competed to map, sequence, and characterize the immunoglobulin loci of mouse and man. Now that this work is near completion, it has become evident that the human and mouse germline repertoires share broad similarities in gene composition, organization, and other general principles. In spite of these similarities, the repertoires expressed by adult mice and humans are distinct and differ from each other in detail. In both species the mechanisms used to create repertoire diversity appear designed to generate a random range of antigen binding sites. However, a detailed analysis reveals significant constraints in the sequence and amino acid composition of the third complementarity region of the H chain (CDR-H3), which lies at the center of the antigen binding site. The mechanisms used to regulate the composition of the repertoire, their significance to the development and maintenance of immune competence, and the contribution of violation of normal repertoire boundaries to the development of diseases of immune function remain foci of ongoing investigation.

Animals↗
PubMed2005

Plant conserved non-coding sequences and paralogue evolution.

Genome duplication is a powerful evolutionary force and is arguably most prominent in plants, where several ancient whole-genome duplication events have been documented. Models of gene evolution predict that functional divergence between duplicates (subfunctionalization) is caused by the loss of regulatory elements. Studies of conserved non-coding sequences (CNSs), which are putative regulatory elements, indicate that plants have far fewer CNSs per gene than mammals, suggesting that plants have less complex regulatory mechanisms. Furthermore, a recent study of a duplicated gene pair in maize suggests that CNSs are lost in a complementary fashion, perhaps driving subfunctionalization. If subfunctionalization is common, one expects duplicate genes to diverge in expression; recent microarray analyses in Arabidopsis thalinia suggest that this is the case. Plant genomes are relatively complex on a genomic level because of the prevalence of whole-genome duplication and, paradoxically, subfunctionalization after duplication can lead to relatively simple regulatory regions on a per gene basis.

Base Sequence↗
PubMed1998

Retrovirus receptor PiT-1 of the Felis catus.

We isolated a cDNA encoding a feline homolog of human PiT-1, a sodium-dependent phosphate symporter which is utilized by gibbon ape leukemia virus (GALV) as a receptor for entry into host cells. The overall homology between the human and feline receptors is 92 and 93% at the nucleotide and deduced amino acid levels, respectively. Hydropathy analyses implied ten potential membrane spanning regions and, in analogy to human and murine homologs, five extracellular and four intracellular loops. Strikingly, the amino acid sequence of the fourth extracellular loop, which is critical for GALV surface glycoprotein binding, has complete identity between the human and feline PiT-1s, while the mouse PiT-1, non-functional for GALV entry, is quite divergent. Ectopic expression of the feline PiT-1 in guinea pig cells, which are non-permissive to feline leukemia virus (FeLV), subgroup B virus, conferred susceptibility to FeLV-B infection confirming the functional ability of the cloned product to serve as a receptor for a natural retrovirus of the homologous species.

Amino Acid Sequence↗
PubMed2002

Cytokine fingerprinting of chemical allergens: species comparisons and statistical analyses.

The cellular and molecular mechanisms that result in the induction of chemical respiratory sensitization are unclear, although there is evidence for the development of T helper (Th) 2 type responses and, in some cases, the production of IgE. We have compared cytokine secretion patterns stimulated by topical exposure of BALB/c strain mice or Brown Norway (BN) strain rats to the reference respiratory allergen trimellitic anhydride (TMA), or to the reference contact allergen 2,4-dinitrochlorobenzene (DNCB). Under conditions where TMA and DNCB provoke similar levels of immune activation [increases in lymph node cell (LNC) cellularity and proliferation] divergent cytokine expression patterns are elicited. TMA-activated LNC isolated from BALB/c mice or BN rats elaborated high levels of the Th2-type cytokines interleukin (IL)-10 and IL-13, but relatively little of the Th1-type cytokines IL-12 or interferon gamma. For LNC derived from both species there was a requirement for restimulation in vitro with the mitogen concanavalin A for IL-4 production. Generally, DNCB-stimulated LNC displayed the converse type 1 cytokine phenotype. The cytokine secretion profiles of LNC isolated from BN rats were considerably more variable than those observed for LNC from BALB/c mice. Statistically significant differences (P<0.01) between DNCB- and TMA-activated LNC were recorded for all cytokines in BALB/c strain mice. For the BN rat, differences reached statistical significance (P<0.01) only for the expression of IL-4 and IL-13. These data demonstrate that the intrinsic ability of DNCB and TMA to promote preferential Th1- and Th2-type responses, respectively, is species-independent and provide further evidence that chemical respiratory allergens are associated with polarized Th2-type responses. For the prospective assessment of chemical respiratory allergens as a function of induced cytokine secretion profiles, however, these data suggest that the use of the BALB/c strain mouse will provide the more robust method.

Allergens↗
PubMed2000

The LAMB1 gene from the clubmoss, Lycopodium annotinum, is a divergent MADS-box gene, expressed specifically in sporogenic structures.

Transcription factors encoded by the large MADS-box gene family have important developmental functions in angiosperms, the flowering plants. Mutations in certain MADS-box genes are known to cause homeotic alterations in floral organ identity, and the establishment of floral organ identity is the most well-studied developmental process in which MADS-box genes are known to function. Our interest is in the potential connection between the duplication history of this gene family and the evolutionary origin of the structures that the different MADS-box genes developmentally regulate in plants. Previous studies have demonstrated that the origin of the MADS-box genes that control floral organ identity predate the evolutionary origin of the flower itself, since gymnosperms have genes that are orthologous to angiosperm floral homeotic MADS-box genes, whereas ferns appear to lack such genes. Here we report on the isolation of a MADS-box gene from Lycopodium annotinum, which belongs to the clubmosses, the phylogenetic sister group to other vascular plants. The gene, LAMB1, in the sporophyte is expressed exclusively in the reproductive structure, the strobilus, during sporogenesis. LAMB1 is similar to other plant MADS-box genes in that it contains a MADS-box as well as a second conserved element, a K-box. However, it differs in length and in exon/intron structure in the region between the MADS- and K-box, and also in the length and structure of the C-terminal region. A phylogenetic analysis indicates that LAMB1 is not closely related to other plant-type MADS-box genes, and may represent one of the basal branches in the phylogenetic tree of plant MADS-box genes.

Amino Acid Sequence↗
PubMed2001

Conserved as well as divergent regulatory elements account for expression of the human and rodent phenylalanine hydroxylase genes.

We have uncovered a fundamental difference in the regulation of the rodent and the human phenylalanine hydroxylase (PAH) genes: expression of human PAH is independent of glucocorticoids and/or cAMP in contrast to the mouse gene which is not only highly inducible but dependent upon hormones for expression. Nevertheless, the two genes do exhibit similarities: DNaseI hypersensitive sites are identically located in the regulatory regions, and the sequences around these sites are partially conserved and associated with regulatory elements sharing similar function. In transient transfections, the human proximal promoter is tissue-specific and presents significant activity compared to the extremely low and ubiquitous activity of the mouse promoter. DNA fragments corresponding to the two upstream hypersensitive sites of both genes have enhancer activity that depends upon the liver-enriched transcription factor binding sites for hepatocyte nuclear factor (HNF) 1 and/or CCAAT/enhancer binding protein (C/EBP). While expression of the rodent gene relies upon two modules in the HSIII enhancer, one activated by HNF1 and C/EBP and the other required for the hormone response, the human equivalent has conserved only the liver-specific transcription factor binding module. Even though the more proximal enhancer is not necessary for full reporter gene activity in transient transfection assays in Pah-expressing hepatoma cells, this enhancer could be required in both species for activation during development.

Animals↗
PubMed1998

Follicular dominance in cattle is associated with divergent patterns of ovarian gene expression for insulin-like growth factor (IGF)-I, IGF-II, and IGF binding protein-2 in dominant and subordinate follicles.

A decrease in insulin-like growth factor (IGF) binding protein (BP) amount occurs within the follicular fluid of dominant ovarian follicles. At the same time, concentrations of follicular fluid IGF-I do not change. The mRNA for IGF-I, IGF-II, IGFBP-2, and IGFBP-3, in dominant and subordinate follicles were measured to determine if changes in IGF or IGFBP gene expression are associated with follicular dominance. Heifers were ovariectomized during a follicular wave, either during early-dominance (emerging dominant follicle, 9 mm diameter) or mid-dominance (established dominant follicle, 14-16 mm diameter). Follicles were classified as either dominant (DF), subordinate (SF), or not-recruited (NRF; small antral follicles). mRNA was localized by in situ hybridization and measured by image analyses. The IGF-I mRNA (granulosa cells) was greatest in DF and increased in DF, SF, and NRF from early- to mid-dominance. Likewise, IGF-II mRNA (theca cells) was greatest in DF compared with SF or NRF. The IGFBP-2 mRNA (granulosa cells), however, was nearly undetectable in DF, whereas adjacent SF expressed abundant IGFBP-2 mRNA. The NRF were not uniform in their IGFBP-2 expression because only 5 of 13 NRF had IGFBP-2 mRNA. The IGFBP-3 mRNA (granulosa cells) was found only in two NRF, suggesting that local synthesis is not a predominant source of follicular fluid IGFBP-3. These data show that changes in gene expression for IGFBP-2 are opposite to those for IGF-I or IGF-II. Increased IGF-I and IGF-II mRNA and decreased IGFBP-2 mRNA within the DF may be one mechanism leading to follicular dominance. The opposite pattern of IGFBP-2 gene expression in SF and some NRF may lead to follicular atresia.

Animals↗