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At least 847 records · Page 47Linked to original sources
PubMed1999

Quantitative alleles of CR1: coding sequence analysis and comparison of haplotypes in two ethnic groups.

The quantitative expression of complement receptor type 1 (CR1) on erythrocytes is regulated by two CR1 alleles that differ in having genomic HindIII fragments of either 7.4 or 6.9 kb and that determine high (H allele) or low (L allele) CR1 expression, respectively, across a 10-fold range. To investigate whether the product of the L allele may contain amino acid substitutions that make it more susceptible to proteolysis, cDNA sequence spanning the CR1 coding region was analyzed in two donors who were homozygous for the H and L alleles and differed by 7-fold in their mean numbers of CR1 per erythrocyte. Sequence differences were detected at 10 nucleotide positions, including 6 that would cause amino acid substitutions. The HindIII RFLP and 3 of the latter 6 sites were analyzed in genomic DNA of 85 Caucasians and 75 African Americans; sites encoding the other amino acid substitutions were analyzed less extensively. Two major haplotypes defined prototypic H and L alleles in both ethnic groups, suggesting that these alleles existed before the African and European populations diverged. Decreased erythrocyte CR1 expression is associated with impaired clearance of immune complexes from blood. Persistence of the L allele in all populations that have been analyzed may suggest a compensatory survival advantage, perhaps related to malaria or another infectious disease.

Alleles↗
PubMed2005

Asymmetric expression of transcripts derived from the shared promoter between the divergently oriented ACACA and TADA2L genes.

The mammalian gene (ACACA) encoding acetyl-CoA carboxylase-alpha, a key regulatory enzyme of fatty acid synthesis, is transcribed from multiple promoters. We have delineated the 5' boundary of ACACA in four species (human, mouse, rat, and ovine). The 5' end of ACACA is located within a 600- to 700-bp CpG island encompassing a bidirectional promoter shared with the divergently oriented TADA2L, which encodes a component of chromatin-modifying complexes. In mouse and rat, this promoter, now referred to as Acaca PI, is located 43 kb upstream of the previously known regulatory regions. The shared promoter coregulates transcripts for TADA2L and ACACA in an asymmetric fashion in human and mouse tissues. A higher concentration of RNA polymerase II (Pol II) within the intergenic region in brain compared to liver of mouse reflects the greater abundance of the two transcripts in brain. The concentration of Pol II tracking downstream, which is lower than at the promoter, is not significantly different in either gene in the two tissues and does not reflect the 10- and >200-fold greater abundance of Tada2l and Acaca PI transcripts, respectively, in brain. Thus, regulation of clearance of Pol II from the promoter and the rate of elongation may therefore be determinants of the asymmetric expression of these transcripts.

Acetyl-CoA Carboxylase↗
PubMed2004

Molecular cloning, structure, expression, and chromosomal localization of the human Osterix (SP7) gene.

We report the isolation of the human orthologue of the mouse Osterix (Osx/Sp7) gene, a C2H2 zinc finger transcription factor of the SP gene family and putative "master" regulator of bone cell differentiation. The human SP7 cDNA encodes a putative 431 amino acid protein that contains three consecutive C2H2 zinc finger repeats. The SP7 protein is highly conserved between mice and humans with an overall sequence identity of 95%. The expression of a SP7 mRNA transcript of approximately 3.2 kb is restricted to bone-derived cell lines in vitro but undetectable in any adult tissues including mandibular bone by Northern blot hybridization. The specific expression of SP7 mRNA in osteoblasts in vivo was further confirmed by in situ hybridization on human embryonic tissues. The highly restricted expression pattern and the divergence of the sequence outside of the zinc finger region distinguish SP7 as a unique member of the SP family. The SP7 gene consists of two exons, with exon 2 containing most of the protein coding sequence. The gene locus was mapped to chromosome 12q13.13 by fluorescent in situ hybridization (FISH). The identification and initial characterization of the SP7 gene will facilitate the study of the molecular regulation of osteoblast differentiation in humans.

Amino Acid Sequence↗
PubMed1995

Differential transcription and expression of ornithine decarboxylase in embryos of replicated mouse lines divergently selected for lean body mass.

Embryos of replicated mouse lines divergently selected for high or low lean body mass have been shown to differ approximately twofold in the activity of ornithine decarboxylase during embryogenesis and that this difference has been shown to be associated with a restriction enzyme polymorphism in the structural gene [Gray and Tait (1993) Genet. Res. 62, 31-37]. In the present paper we report that the differences in enzyme activity are due to changes in transcription and show that the enzyme produced has the same specific activity in all selected lines, precluding any significant structural change in the enzyme being associated with the differences in the structural gene.

Animals↗
PubMed1998

Isolation and characterization of mammalian homologs of the Drosophila gene glial cells missing.

The glial cells missing (gcm) gene in Drosophila encodes a transcription factor that determines the choice between glial and neuronal fates. We report here the isolation of two mammalian gcm homologs, Gcm1 and Gcm2, and the characterization of their expression patterns during embryonic development. Although Gcm2 is expressed in neural tissues at a low level, the major sites of expression for both of the mammalian genes are nonneural, suggesting that the functions of the mammalian homologs have diverged and diversified. However, when expressed ectopically, Gcm1 can substitute functionally for Drosophila gcm by transforming presumptive neurons into glia. Thus, certain biochemical properties, although not the specificity of the tissue in which the gene is expressed, have been conserved through the evolution of the Gcm gene family.

Amino Acid Sequence↗
PubMed1998

The narA locus of Synechococcus sp. strain PCC 7942 consists of a cluster of molybdopterin biosynthesis genes.

The narA locus required for nitrate reduction in Synechococcus sp. strain PCC 7942 is shown to consist of a cluster of genes, namely, moeA, moaC, moaD, moaE, and moaA, involved in molybdenum cofactor biosynthesis. The product of the moaC gene of strain PCC 7942 shows homology in its N-terminal half to MoaC from Escherichia coli and in its C-terminal half to MoaB or Mog. Overexpression of the Synechococcus moaC gene in E. coli resulted in the synthesis of a polypeptide of 36 kDa, a size that would conform to a protein resembling a fusion of the MoaC and MoaB or Mog polypeptides of E. coli. Insertional inactivation of the moeA, moaC, moaE, and moaA genes showed that the moeA-moa gene cluster is required for growth on nitrate and expression of nitrate reductase activity in strain PCC 7942. The moaCDEA genes constitute an operon which is transcribed divergently from the moeA gene. Expression of the moeA gene and the moa operon was little affected by the nitrogen source present in the culture medium.

Coenzymes↗
PubMed2001

Region-specific transcriptional response to chronic nicotine in rat brain.

Even though nicotine has been shown to modulate mRNA expression of a variety of genes, a comprehensive high-throughput study of the effects of nicotine on the tissue-specific gene expression profiles has been lacking in the literature. In this study, cDNA microarrays containing 1117 genes and ESTs were used to assess the transcriptional response to chronic nicotine treatment in rat, based on four brain regions, i.e. prefrontal cortex (PFC), nucleus accumbens (NAs), ventral tegmental area (VTA), and amygdala (AMYG). On the basis of a non-parametric resampling method, an index (called jackknifed reliability index, JRI) was proposed, and employed to determine the inherent measurement error across multiple arrays used in this study. Upon removal of the outliers, the mean correlation coefficient between duplicate measurements increased to 0.978+/-0.0035 from 0.941+/-0.045. Results from principal component analysis and pairwise correlations suggested that brain regions studied were highly similar in terms of their absolute expression levels, but exhibited divergent transcriptional responses to chronic nicotine administration. For example, PFC and NAs were significantly more similar to each other (r=0.7; P<10(-14)) than to either VTA or AMYG. Furthermore, we confirmed our microarray results for two representative genes, i.e. the weak inward rectifier K(+) channel (TWIK-1), and phosphate and tensin homolog (PTEN) by using real-time quantitative RT-PCR technique. Finally, a number of genes, involved in MAPK, phosphatidylinositol, and EGFR signaling pathways, were identified and proposed as possible targets in response to nicotine administration.

Amygdala↗
PubMed2004

Differential expression of iodothyronine deiodinase type 2 in growth plates of chickens divergently selected for incidence of tibial dyschondroplasia.

Tibial dyschondroplasia (TD) is a genetic leg defect in broilers with a lesion of avascular, non-calcified cartilage below the growth plate of the proximal tibiatarsus. This disease is considered to result from the inability of chondrocytes to undergo terminal differentiation. Thyroid hormones are required for chondrocyte differentiation. The thyroid gland produces and secrets mostly L-thyroxine or T4 and T4 plays most of its biological activities through conversion to triiodothyronine or T3 in local tissues by iodothyronine deiodinases type 1 or type 2, which are tissue specific. In this study, no differences were found in the plasma concentrations of total T3 and T4 between two chicken lines divergently selected for the incidence of TD. Plasma T4 was higher than T3, especially in older chickens. Younger birds had much higher T3 than older birds, but there were no significant age differences in T4. The expression level of deiodinase type 2 in the growth plates of broilers with TD was one-eighth of those birds without the disease. The expression levels of deiodinase type 2 (DIO2) in commercial broilers without the disease were much higher than those with TD and lower than those without the disease in the susceptible and resistant lines, respectively. These results indicate that the inadequate expression of DIO2 in the growth plates contributes to the pathogenesis of TD in broilers and that TD is a tissue-specific hypothyroidism.

Animals↗
PubMed2026

The domestication-associated WHP10 tandem cluster of amino acid transporter genes enhances whole-plant protein accumulation in maize.

Improving protein accumulation in maize is essential for sustainable agriculture, yet the regulatory mechanisms governing the intermediate "flow" of organic nitrogen remain elusive. Here, we show that the maize stem acts as a regulatory node for nitrogen allocation. By integrating spatial transcriptomics and metabolomics with quantitative genetics, we demonstrate that a transport-oriented stem program orchestrates the high-protein phenotype of the wild maize accession Ames21814. We identified a major locus, Whole-plant High Protein 10 (WHP10), that encodes a tandemly duplicated cluster of amino acid transporter genes. WHP10 exhibits strong vascular-biased expression, driven by promoter divergence that enhances the wild allele's activity. Functional assays and genetic validation support a model in which the WHP10 cluster facilitates the transport of multiple nitrogen-rich amino acids, thereby contributing to vascular-associated amino acid transport and post-uptake organic-nitrogen partitioning. Our findings establish stem flow as a regulatory layer for protein accumulation and identify WHP10 as a high-value target for precision breeding to enhance whole-plant protein accumulation without compromising grain yield.

Zea mays↗
PubMed1985

Regulation of Ti plasmid virulence genes by a chromosomal locus of Agrobacterium tumefaciens.

We isolated a mutant strain of Agrobacterium tumefaciens, designated Ros, that has a pleiotropic phenotype which includes elevated levels of expression of certain genes in the virulence (Vir) region of tumor-inducing plasmid pTiC58. This mutant and others were isolated by fusing the promoter of the Vir bak gene to a promoterless gene (cat) that encodes chloramphenicol acetyltransferase and then selecting for increased expression of cat in A. tumefaciens. The ros mutation is chromosomal in nature and is characterized by a more-than-300-fold increase in the level of expression of bak and a 12-fold increase in the level of expression of an adjacent divergent operon containing the hdv genes, which are involved in some aspect of host specificity. The Ros mutant is fully virulent and is typified by its unusual colony morphology; the colonies have rough surfaces, uneven edges, and a pit in the center at 24 degrees C and vary markedly in appearance from one growth temperature to another. The Ros mutant is not able to form colonies at 12 degrees C, a temperature at which the wild-type strain forms colonies in 14 days. The ros mutation occurs spontaneously with a frequency of 5 X 10(-8). Genetic and biochemical evidence indicates that the product of the ros locus is a negative regulator of Ti plasmid genes and is related to undefined chromosomally encoded functions that are involved in the mutant phenotype.

Chromosomes, Bacterial↗
PubMed1996

A functional homologue of goosecoid in Drosophila.

We have cloned a Drosophila homologue (D-gsc) of the vertebrate homeobox gene goosecoid (gsc). In the Gsc proteins, the pressure for conservation has been imposed on the homeodomain, the functional domain of the protein: sequence homology is limited to the homeodomain (78% identity) and to a short stretch of 7 aminoacids also found in other homeoproteins such as Engrailed. Despite this weak homology, D-gsc is able to mimic gsc function in a Xenopus assay, as shown by its ability to rescue the axis development of a UV-irradiated embryo. Moreover, our data suggest that the position of insect and vertebrate gsc homologues within a regulatory network has also been conserved: D-gsc expression is controlled by decapentaplegic, orthodenticle, sloppy-paired and tailless whose homologues control gsc expression (for BMP4 and Otx-2), or are expressed at the right time and the right place (for XFKH1/Pintallavis and Tlx) to be interacting with gsc during vertebrate development. However, the pattern of D-gsc expression in ectodermal cells of the nervous system and foregut cannot easily be reconciled with that of vertebrate gsc mesodermal expression, suggesting that its precise developmental function might have diverged. Still, this comparison of domains of expression and functions among Gsc proteins could shed light on a common origin of gut formation and/or on basic cellular processes. The identification of gsc target genes and/or other genes involved in similar developmental processes will allow the definition of the precise phylogenetic relationship among Gsc proteins.

Amino Acid Sequence↗
PubMed2006

Unique sequence and expression profiles of rat galectins-5 and -9 as a result of species-specific gene divergence.

Presence of species-specific gene divergence in a protein family prompts to thoroughly study structural aspects and expression profiles of the products. We herein focus on two members of an adhesion/growth-regulatory group of endogenous lectins, i.e. galectins-5 and -9. After first ascertaining species specificity of occurrence of galectin-5, constituted by a short section of rat galectin-9's N-terminal part and its C-terminal carbohydrate recognition domain, by database mining, we next detected and defined sequence differences in the proximal promoter region between the two genes. The ensuing hypothesis for distinct expression profiles was tested first by RT-PCR and then by immunohistochemistry. For the latter purpose, we employed antibodies rigorously controlled for absence of cross-reactivity including assays with various other galectins and, if necessary, refined by chromatographic removal of bi- or oligospecific activities. Indeed, the galectins have non-identical expression profiles, qualitative differences, e.g. seen for galectin-5-positive bone marrow and erythrocytes or for hitherto unknown expression in cells of the theca folliculi and galectin-9-positive skin epidermis and esophageal epithelium. Lack of hepatocyte or renal cortex staining separates these two expression profiles in rat from localization of galectin-9 in mouse. Interspecies extrapolation in a case of a galectin involved in unique gene divergence may thus not be valid. The presented results on galectin-5 relative to galectin-9 intimate distinct functions especially in erythropoiesis and imply currently unknown mechanisms to compensate its absence from the galectin network in other mammals.

Amino Acid Sequence↗
PubMed1997

Phylogenetic analysis of glycolytic enzyme expression.

Although differences among species in enzyme maximal activity or concentration are often interpreted as adaptive and important for regulating metabolism, these differences may simply reflect phylogenetic divergence. Phylogenetic analysis of the expression of the glycolytic enzymes among 15 taxa of a North American fish genus (Fundulus) indicated that most variation in enzyme concentration is due to evolutionary distance and may be nonadaptive. However, three enzymes' maximal activities covary with environmental temperature and have adaptive value. Additionally, two pairs of enzymes covary, indicating coevolution. Thus, metabolic flux may be modulated by many different enzymes rather than by a single rate-limiting enzyme.

Adaptation, Physiological↗
PubMed2003

Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia.

Wigglesworthia glossinidia brevipalpis, the obligate bacterial endosymbiont of the tsetse fly Glossina brevipalpis, is characterized by extreme genome reduction and AT nucleotide composition bias. Here, multivariate statistical analyses are used to test the hypothesis that mutational bias and genetic drift shape synonymous codon usage and amino acid usage of Wigglesworthia. The results show that synonymous codon usage patterns vary little across the genome and do not distinguish genes of putative high and low expression levels, thus indicating a lack of translational selection. Extreme AT composition bias across the genome also drives relative amino acid usage, but predicted high-expression genes (ribosomal proteins and chaperonins) use GC-rich amino acids more frequently than do low-expression genes. The levels and configuration of amino acid differences between Wigglesworthia and Escherichia coli were compared to test the hypothesis that the relatively GC-rich amino acid profiles of high-expression genes reflect greater amino acid conservation at these loci. This hypothesis is supported by reduced levels of protein divergence at predicted high-expression Wigglesworthia genes and similar configurations of amino acid changes across expression categories. Combined, the results suggest that codon and amino acid usage in the Wigglesworthia genome reflect a strong AT mutational bias and elevated levels of genetic drift, consistent with expected effects of an endosymbiotic lifestyle and repeated population bottlenecks. However, these impacts of mutation and drift are apparently attenuated by selection on amino acid composition at high-expression genes.

Amino Acids↗
PubMed2001

Two ResD-controlled promoters regulate ctaA expression in Bacillus subtilis.

The Bacillus subtilis ResDE two-component system plays a positive role in global regulation of genes involved in aerobic and anaerobic respiration. ctaA is one of the several genes involved in aerobic respiration that requires ResD for in vivo expression. The ctaAB-divergent promoter regulatory region has three ResD binding sites; A1, A2, and A3. The A2 site is essential for in vivo promoter activity, while binding sites A2 and A3 are required for full ctaA promoter activity. In this study, we demonstrate the role of ResD~P in the activation of the ctaA promoter using an in vitro transcription system. The results indicate that the ctaA promoter (binding sites A2 and A3) has two transcriptional start sites. Binding site A2 was sufficient for weak transcription of the upstream promoter (Pv) by Esigma(A), transcription which was enhanced approximately 1.5-fold by ResD and 5-fold by ResD~P. The downstream promoter (Ps) required both binding sites A2 and A3 and was not transcribed by Esigma(A) with or without ResD~P. RNA polymerase (RNAP) isolated from B. subtilis when cells were at the end of exponential growth (T(0)) or 3, 4, or 5 h into the stationary phase (T(3), T(4), or T( 5), respectively) was used in in vitro transcription assays. Maximal transcription from Ps required T(4) RNAP plus ResD~P. RNAP isolated from a spo0A or a sigE mutant strain was not capable of Ps transcription. Comparison of the Ps promoter sequence with the SigE binding consensus suggests that the ctaA Ps promoter may be a SigE promoter. The collective data from ResD footprinting, in vivo promoter deletion analysis, and in vitro transcription assays suggest that ctaA is transcribed during late exponential to early stationary phases of growth from the Pv promoter, which requires ResD binding site A2, Esigma(A), and ResD~P, and during later stationary phase from Ps, which requires binding sites A2 and A3, ResD~P, and Esigma(E) or a sigma factor whose transcription is dependent on SigE.

Aerobiosis↗
PubMed2006

The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages.

BACKGROUND: In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution.Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific expansion patterns? We also looked for correlations between relative EST database representation in Arabidopsis and similarity to orthologs in early lineages. RESULTS: Homologs of all seven MST subfamilies were present in land plants at least 400 million years ago. Subfamily expression levels vary across lineages with greater relative expression of the STP, ERD6-like, INT and PLT subfamilies in the vascular plants. In the large EST databases of the moss, gymnosperm, monocot and eudicot lineages, EST contig construction reveals that MST subfamilies have experienced lineage-specific expansions. Large subfamily expansions appear to be due to multiple gene duplications arising from single ancestral genes. In Arabidopsis, one or a few genes within most subfamilies have much higher EST database representation than others. Most highly represented (broadly expressed) genes in Arabidopsis have best match orthologs in early divergent lineages. CONCLUSION: The seven subfamilies of the Arabidopsis MST gene family are ancient in land plants and show differential subfamily expression and lineage-specific subfamily expansions. Patterns of gene expression in Arabidopsis and correlation of highly represented genes with best match homologs in early lineages suggests that broadly expressed genes are often highly conserved, and that most genes have more limited expression.

Arabidopsis↗
PubMed2002

Expression and localization of the homeodomain-containing protein HEX in human thyroid tumors.

Homeobox genes are involved in neoplastic transformation of both epithelial and hemopoietic tissues. The divergent homeobox gene HEX is expressed in the anterior visceral endoderm during early mouse development and in some adult tissues of endodermal origin, including liver and thyroid. Whereas a role in leukemyogenesis has been proposed already, few data are available on the involvement of HEX in human epithelial tumors. Herein, we analyzed HEX expression and subcellular localization in a series of 55 human thyroid tumors and in several tumoral cell lines. HEX mRNA was detected by RT-PCR either in normal tissues or in thyroid adenomas and differentiated (papillary and follicular) carcinomas. HEX mRNA was also expressed in most undifferentiated carcinomas. Subcellular localization of HEX protein was investigated by immunohistochemistry. In normal tissues and adenomas, HEX protein was present both in nucleus and cytoplasm. In contrast, both differentiated and undifferentiated carcinomas, as well as the tumoral cell lines investigated, showed HEX protein only in the cytoplasm. These findings suggest that regulation of HEX entry in the nucleus of thyrocytes may represent a critical step during human thyroid tumorigenesis.

Cell Nucleus↗
PubMed1997

Cyclin-D1-gene amplification and expression in breast carcinoma: relation with clinicopathologic characteristics and with retinoblastoma gene product, p53 and p21WAF1 immunohistochemical expression.

Cyclin D1 is a major positive regulator of the G1 restriction point promoting inactivation of the retinoblastoma protein (RB). The cyclin D1 gene is rearranged, amplified and/or over-expressed in several human neoplasms. In the present series of 64 human breast carcinomas, cyclin D1 amplification (4- to 8-fold) was seen in 24% of cases, and cyclin-D1 immunohistochemical over-expression was seen in 50% of cases. Amplification and over-expression were statistically associated; however, divergent result were seen in 30% of cases. Some of these discrepancies may reflect the fact that cyclin-D1 expression may be due to mechanisms other than gene amplification. Cyclin-D1 over-expression, but not cyclin-D1 amplification, was associated with positive oestrogen-receptor immunoreactivity. Cyclin-D1 amplification was associated with high RB expression, and 4 cases (7%) with absent RB immunoreactivity showed no cyclin-D1 amplification nor expression. Our data support the hypothesis that cyclin-D1 amplification may be associated with enhanced gene transcription and with high RB expression, that high ER expression may cooperate in maintaining high levels of cyclin-D1 protein, and that loss of RB function, as assessed by the lack of RB immunoreactivity, may be related to normal cyclin-D1 gene copy number and low cyclin-D1 expression.

Blotting, Southern↗