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At least 343 records · Page 19Linked to original sources
PubMed1990

Chimeric genes and transgenic plants are used to study the regulation of genes involved in symbiotic plant-microbe interactions (nodulin genes).

Nodulin genes are plant genes specifically activated during the formation of nitrogen-fixing nodules on leguminous plants. These genes are interesting to study since they are not only induced in a specific developmental fashion by signals coming directly or indirectly from the rhizobial symbiont, but are also expressed in a tissue-specific manner. By examining the expression of chimeric nodulin-reporter genes in transgenic legume plants it has been shown that nodule specific expression is mediated by DNA sequences present in the 5 upstream region of several nodulin genes. Here we summarize the available data on these cis-acting elements and the trans-acting factors interacting with them. We also review experiments designed to identify rhizobial "signals" which may play a role in nodule specific gene expression.

Base Sequence↗
PubMed1998

Gene 1, one of the dna genes of bacteriophage phi 29, represses other dna genes through binding to mRNA.

The dna genes, essential for protein priming DNA replication of bacteriophage phi 29, are transcribed as a long polycistronic mRNA. In the previous study, gene 1 product (gp1) was shown to repress the expression of the upstream dna genes for DNA polymerase and primer protein. To investigate the details of the repression by gp1, we have examined the amount and integrity of polycistronic mRNA encoding DNA polymerase and primer protein by agarose gel electrophoresis and nuclease S1 protection assay. As a result, the amount, size, and integrity of the polycistronic mRNA were not influenced by the presence of gene 1. Furthermore, the RNA binding ability of gp1 was demonstrated by in vitro system using histidine-tagged gp1. These results strongly suggested that translation of the dna genes was affected by gp1 through binding to mRNA. Other possible mechanisms of gene regulation by gp1 were discussed.

Bacillus Phages↗
PubMed1999

Gene function, gene networks and the fate of duplicated genes.

For both copies of a duplicated gene to become fixed in a population and subsequently maintained, selection must favour individuals with both genes over individuals with one. Here I review and assess some of the proposed ways that gene structure and function might affect the likelihood of both copies acquiring distinct functions and therefore positive selection. In particular I focus on the interacting pathways of genes that make up gene networks, and how these may affect genes duplicated both singly and en masse. Using the Wnt and hedgehog pathways as examples and data from developmental and genome analyses, I show that, while some of these theories may genuinely reflect what has occurred in animal evolution, there are still insufficient data to rigorously assess their relative importance. This, however, is likely to change in the near future.

Animals↗
PubMed1998

A novel member of the bombyxin gene family: structure and expression of bombyxin G1 gene, an insulin-related peptide gene of the silkmoth Bombyx mori.

Bombyxin G1 gene, a novel insulin-related peptide gene of the silkmoth Bombyx mori, has been identified. The G1 gene encodes a precursor peptide which shows 41-56% and 28% sequence identities with preprobombyxins previously characterized and human preproinsulin, respectively. The G1 gene forms a pair with bombyxin C2 gene with opposite transcriptional orientation in a bombyxin gene cluster. The bombyxin G1 mRNA in Bombyx brain was shown to locate in four pairs of medial neurosecretory cells.

Amino Acid Sequence↗
PubMed2005

Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions.

In rice, at the stage from pistil and stamen primordia formation to microsporocyte meiosis, the young panicle organs (YPO) make a great contribution to grain productivity. This period corresponds to the onset of meiosis and marks the transition from vegetative to reproductive stages. By comparing gene expression profiling of YPO with that of rice aerial vegetative organs (AVO), it is possible to gain further molecular insight into this period that is developmentally and functionally important. In this report, a total of 92,582 high-quality ESTs from 5'-end sequencing, including 44,247 from YPO and 48,335 from AVO, were obtained and classified. There were 12,884 (29.12%) ESTs from YPO and 16,304 (33.73%) ESTs from AVO matched to known genes, which generated 1,667 and 2,172 known genes, respectively, after integration of these ESTs. From the functions of known homologous genes, we identified some tissue- and developmental-stage-specified genes in YPO. The expression of these genes clearly reflected the unique functional characteristics of YPO. Furthermore, we estimated that there are about 10,000 mRNAs specifically expressed in rice YPO.

DNA Primers↗
PubMed1992

Gene translocations in poxviruses: the fowlpox virus thymidine kinase gene is flanked by 15 bp direct repeats and occupies the locus which in vaccinia virus is occupied by the ribonucleotide reductase large subunit gene.

By sequencing a fragment of 7351 bp the fowlpox virus thymidine kinase gene has been found to map to a position within the equivalent of the vaccinia HindIII I fragment. The deduced gene arrangement in fowlpox virus is I3, X, TK, I5, I6, I7, I8, G1, indicating that the homologue of the vaccinia I4 gene has been replaced by two genes X and TK. The non-essential TK gene has therefore replaced another non-essential gene, I4 (the ribonucleotide reductase large subunit) in this region. The X/TK insertion in fowlpox virus is precisely flanked by direct repeats of 15 bp suggesting that the translocation event may have involved transposition. The % identities between the fowlpox virus and vaccinia virus proteins ranged between 58.5% and 31.3%.

Amino Acid Sequence↗
PubMed2002

A gene trap Dissociation insertion line, associated with a RING-H2 finger gene, shows tissue specific and developmental regulated expression of the gene in Arabidopsis.

Real interesting new gene (RING) finger proteins act as E3 ubiquitin-protein ligases and play critical roles in targeting the destruction of proteins of diverse functions in all eukaryotes, ranging from yeast to mammals. Arabidopsis genome contains a large number of genes encoding RING finger proteins. In this report we describe the identification of more than 40 RING-H2 finger proteins that are of small size, not more than 200 amino acids, and contain no other recognizable protein-protein interaction domain(s). We characterize RHA2b, one of these small RING-H2 finger genes. A gene trap line, SGT6304, was identified to contain a Dissociation (Ds) insertion in RHA2b gene. No RHA2b transcript was detected in the homozygous SGT6304 plants. Despite the elimination of RHA2b function, homozygous SGT6304 plants lacked detectable growth or development defects, suggesting functional redundancy of RHA2b with other RING finger genes. Expression of RHA2b was specifically active in vascular tissue and in upper pistil of inflorescence as well as in root tip and shoot apical meristem region. Potential functions of ubiquitin-proteolysis pathway in vascular formation and in fertilization are discussed.

Amino Acid Sequence↗
PubMed2000

Structure of the mouse type XV collagen gene, Col15a1, comparison with the human COL15A1 gene and functional analysis of the promoters of both genes.

Isolation and characterization of the mouse gene for the alpha1 chain of type XV collagen (Col15a1) revealed it to be approximately 110 kb in length and contain 40 exons. Analysis of the proximal 5'-flanking region showed properties characteristic of a housekeeping gene promoter, such as an absence of TATA and CAAT boxes, the presence of several transcriptional start sites and a high G+C content. The general organization of the mouse Col15a1 gene was found to be highly similar to that of its human homologue, but the genomic area encoding the end of the N-terminal non-collagenous domain showed marked divergence from the human form. Furthermore, two exons coding for the N-terminal collagenous domain of the human alpha1(XV) chain are lacking in the mouse Col15a1 gene. Due to the lack of two exons and a codon divergence in one exon, the mouse alpha1(XV) chain contains seven collagenous domains, whereas the human equivalent contains nine. Comparison of 5'-flanking sequences indicated four domains that were conserved between the mouse and human genes. Functional analysis of the mouse promoter identified cis-acting elements for both positive and negative regulation of Col15a1 gene expression in mouse NIH/3T3 cells.

3T3 Cells↗
PubMed2002

Identification of genes enhanced by protein-calorie malnutrition by differential display polymerase chain reaction (expression of fibrinogen B beta chain, B cell translocation gene 1 and thyroid hormone responsive protein genes).

Protein-calorie malnutrition (PCM), as one of global health problems, arises during protein and/or energy deficit due to disease and nutritional inadequacy. Previously, we showed that PCM elicited oxidative stress with activation of the phase II detoxifying gene expression, which was reversed by cysteine supplementation. As part of the attempts to identify the cellular adaptive responses and the associated gene expression during PCM, the current study was initiated to analyze the genes differentially expressed in the rat during PCM. Among 1,916 bands amplified, 85 putative differentially amplified bands were enhanced by PCM in the liver, while the expression of 64 bands was suppressed. Northern and/or reverse transcription-polymerase chain reaction (RT-PCR) analyses revealed that PCM increased the expression of fibrinogen B beta chain, B cell translocation gene I (BTGI) and thyroid hormone responsive protein (THRP) mRNAs. The increase in the hepatic fibrinogen B beta chain mRNA was not prevented by cysteine supplementation, whereas cysteine decreased the enhancement in the rGSTA2 and microsomal epoxide hydrolase mRNA expression. Cysteine was also active in reversing the increase in BTG1 mRNA during PCM. This was supported by the increase in BTG1 mRNA in H4IIE cells exposed to sulfur amino acid-deprived medium. Northern blot analysis revealed that THRP, highly expressed in the brain in a tissue-specific manner, was induced by PCM and that cysteine supplementation abolished the THRP induction. Conversely, the level of hepatic albumin mRNA was markedly decreased by PCM, which was partially restored by cysteine supplementation. Differential display RT-PCR analysis allowed us to identify the genes that are responsive to oxidative stress during PCM and to characterize the differential role of cysteine on the expression of the fibrinogen B beta chain, BTG1 and THRP genes as a homeostatic adaptive response during protein deficiency.

Adaptor Proteins, Signal Transducing↗
PubMed2004

The porcine taurochenodeoxycholic acid 6alpha-hydroxylase (CYP4A21) gene: evolution by gene duplication and gene conversion.

Porcine taurochenodeoxycholic acid 6alpha-hydroxylase, cytochrome P450 4A21 (CYP4A21), differs from other members of the CYP4A subfamily in terms of structural features and catalytic activity. CYP4A21 participates in the formation of hyocholic acid, a species-specific primary bile acid in the pig. The CYP4A21 gene was investigated and found to be approx. 13 kb in size and split into 12 exons. The intron-exon organization of the CYP4A21 gene corresponds to that of CYP4A fatty acid hydroxylase genes in other species. Comparison with a genomic segment of a pig CYP4A fatty acid hydroxylase gene ( CYP4A24 ) revealed a sequence identity with CYP4A21 that extends beyond the exons, indicating a common origin by gene duplication. A pronounced sequence identity was found also within the proximal 5'-flanking regions, whereas the patterns of mRNA expression of CYP4A21 and CYP4A fatty acid hydroxylases in pig liver differ. Sequence comparison aiming to elucidate the origin of the unique features of CYP4A21 revealed a region of decreased sequence identity from exon 6 to exon 8, strongly suggesting that gene conversion could have contributed to the evolution of CYP4A21.

5' Flanking Region↗
PubMed2002

The HAT2 gene, a member of the HD-Zip gene family, isolated as an auxin inducible gene by DNA microarray screening, affects auxin response in Arabidopsis.

The plant hormone, auxin, regulates many aspects of growth and development. Despite its importance, the molecular mechanisms underlying the action of auxin are largely unknown. To gain a more comprehensive understanding of the primary responses to auxin, we analyzed the expression of genes in Arabidopsis seedlings treated with indole-3-acetic acid (IAA) for 15 min. We identified a single gene that is downregulated early, and 29 genes that are upregulated early. Several types of typical transcription factors are identified as early upregulated genes, suggesting that auxin signals are mediated by a master set of diverse transcriptional regulators. Of the genes that responded to auxin, the expression of the homeobox gene, HAT2, was induced rapidly. Furthermore, we show that the expression of HAT2 is induced by auxin, but not by other phytohormones. To analyze the function of HAT2 in the plant's response to auxin, we generated 35S::HAT2 transgenic plants. These produced long hypocotyls, epinastic cotyledons, long petioles, and small leaves, which are characteristic of the phenotypes of the auxin-overproducing mutants, superroot1 (sur1) and superroot2 (sur2). On the other hand, 35S::HAT2 plants showed reduced lateral root elongation, and reduced auxin sensitivity compared to wild-type plants. Together with the results of RNA blotting and biochemical analyses, these findings suggest that HAT2 plays opposite roles in the shoot and root tissues in regulating auxin-mediated morphogenesis.

Amino Acid Sequence↗
PubMed1998

The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining.

MOTIVATION: To make effective use of the vast amounts of expressed sequence tag (EST) sequence data generated by the Merck-sponsored EST project and other similar efforts, sequences must be organized into gene classes, and scientists must be able to 'mine' the gene class data in the context of related genomic data. RESULTS: This paper presents the Merck Gene Index browser, an easily extensible, World Wide Web-based system for mining the Merck Gene Index (MGI) and related genomic data. The MGI is a non-redundant set of clones and sequences, each representing a distinct gene, constructed from all high-quality 3' EST sequences generated by the Merck-sponsored EST project. The MGI browser integrates data from a variety of sources and storage formats, both local and remote, using an eclectic integration strategy, including a federation of relational databases, a local data warehouse and simple hypertext links. Data currently integrated include: LENS cDNA clone and EST data, dbEST protein and non-EST nucleic acid similarity data, WashU sequence chromatograms. Entrez sequence and Medline entries, and UniGene gene clusters. Flatfile sequence data are accessed using the Bioapps server, an internally developed client-server system that supports generic sequence analysis applications. Browser data are retrieved and formatted by means of the Bioinformatics Data Integration Toolkit (B-DIT), a new suite of Perl routines.

Abstracting and Indexing↗
PubMed1988

Cloning and physical mapping of RNA polymerase genes from Methanobacterium thermoautotrophicum and comparison of homologies and gene orders with those of RNA polymerase genes from other methanogenic archaebacteria.

The structural genes encoding the four largest subunits of RNA polymerase, A, B', B", and C, were physically mapped in Methanobacterium thermoautotrophicum Winter. The genes formed a cluster in the order B", B', A, C and had a common orientation. DNA hybridization experiments yielded different degrees of homology between RNA polymerase gene sequences of different species of Methanobacterium and Methanococcus voltae. No homology was detectable between Methanobacterium thermoautotrophicum and Methanosarcina barkeri. From Southern hybridization experiments in which probes of the four genes from Methanobacterium thermoautotrophicum Winter and restriction digests of the genomic DNAs of the different methanogens were used, a common gene order of the RNA polymerase genes could be deduced.

Archaea↗
PubMed2004

Effect of SNPs in protein kinase C zeta gene on gene expression in the reporter gene detection system.

AIM: To investigated the effects of the SNPs (rs411021, rs436045, rs427811, rs385039 and rs809912) on gene expression and further identify the susceptibility genes of type 2 diabetes. METHODS: Ten allele fragments (49 bp each) were synthesized according to the 5 SNPs mentioned above. These fragments were cloned into luciferase reporter gene vector and then transfected into HepG2 cells. The activity of the luciferase was assayed. Effects of the SNPs on RNA splicing were analyzed by bioinformatics. RESULTS: rs427811T allele and rs809912G allele enhanced the activity of the reporter gene expression. None of the 5 SNPs affected RNA splicing. CONCLUSION: SNPs in protein kinase Cz (PKCZ) gene probably play a role in the susceptibility to type 2 diabetes by affecting the expression level of the relevant genes.

Base Sequence↗
PubMed1994

The human papillomavirus type 16 E5 gene cooperates with the E7 gene to stimulate proliferation of primary cells and increases viral gene expression.

The E5 gene from HPV-16 has recently been shown to stimulate anchorage-independent growth of murine 3T3 cells and this phenotype was enhanced in the presence of epidermal growth factor (EGF). Since EGF is capable of stimulating cellular signal transduction, we have compared levels of EGF-induced c-fos and c-jun mRNA in E5-expressing 3T3 cells. We present data showing that the expression of c-fos and c-jun was higher in E5-expressing 3T3 cells than in control cells. Complexes of c-fos/c-jun constitute the AP1 transcription factor and the HPV-16 promoter/enhancer contains AP1 enhancer elements. HPV-16 promoter activity was therefore examined in cells transfected with the E5 gene and data are presented which reveal that the viral enhancer is more active in E5-expressing cells. Since the viral E7 gene product has been shown to cooperate with v-fos and certain growth factors for transformation and stimulation of DNA synthesis, we investigated the possible cooperation between E5 and E7 to induce cell proliferation. Transfection of E5 and E7 genes into primary rodent epithelial cells produced a potent mitogenic response which was enhanced in the presence of EGF. These results suggest that E5 may cooperate with the E7 gene to stimulate cell proliferation in vivo.

3T3 Cells↗
PubMed1992

Identification of RAD16, a yeast excision repair gene homologous to the recombinational repair gene RAD54 and to the SNF2 gene involved in transcriptional activation.

The RAD54 gene of Saccharomyces cerevisiae is involved in the recombinational repair of DNA damage. The predicted amino acid sequence of the RAD54 protein shows significant homologies with the yeast SNF2 protein, which is required for the transcriptional activation of a number of diversely regulated genes. These proteins are 31% identical in a 492-amino acid region that includes presumed nucleotide and Mg2+ binding sites. We noted previously that the SNF2 protein also shares homology with a partial open reading frame (ORF) that was reported with the sequence of an adjacent gene. This ORF also shares homology with the RAD54 protein. To test whether this ORF is involved in transcriptional activation or DNA repair, yeast strains deleted for part of it have been isolated. These strains do not show a Snf-like phenotype, but they are UV sensitive. This gene has been identified as RAD16, a gene involved in the excision repair of DNA damage. Analysis of the rad16 deletion mutations indicates that RAD16 encodes a non-essential function and is not absolutely required for excision repair. Outside the region of homology to RAD54 and SNF2, the predicted RAD16 protein contains a novel cysteine-rich motif that may bind zinc and that has been found recently in eleven other proteins, including the yeast RAD18 protein. The homologies between RAD16, RAD54 and SNF2 are also shared by several additional, recently isolated yeast and Drosophila genes.

Adenosine Triphosphatases↗
PubMed1994

Gene replacement of the p53 gene with the lacZ gene in mouse embryonic stem cells and mice by using two steps of homologous recombination.

Two steps of gene targeting were used to replace the p53 gene with the E. coli beta-galactosidase (lacZ) gene in mouse embryonic stem (ES) cells. The first targeting vector consisted of neo and herpes simplex virus thymidine kinase (HSV-tk) genes as a neo-tk cassette in the middle of the targeting vector. At the first targeting, the homologous recombinants became G418 resistant and ganciclovir (GANC) sensitive and were selected by G418 alone. At the second targeting, homologous recombination reciprocally exchanged the neo-tk casette in the ES cell chromosome with the lacZ fragment in the second targeting vector and thus made the ES cells GANC resistant. We obtained two ES cell clones, in which the p53 gene for both had been replaced with a totally non-homologous sequence of the lacZ gene. The germ-line transmission of the manipulated ES cells also demonstrated that the entire procedure had no detrimental effects on ES cells at all.

Animals↗
PubMed2001

Rice ESTs with disease-resistance gene- or defense-response gene-like sequences mapped to regions containing major resistance genes or QTLs.

The chromosomal locations of 109 rice expressed sequence tags (ESTs) in the rice genome were determined using a doubled haploid mapping population. These ESTs show high similarity to disease resistance genes or to defense response genes. Nine of the ESTs were mapped to three regions that contain genetically defined resistance genes on chromosomes 6 and 11. Clustering of the ESTs in the rice genome was observed at several chromosomal regions. Some of the clusters were located in regions where quantitative trait loci (QTL) associated with partial resistance to rice blast, bacterial blight and sheath blight are known to lie. Three ESTs that were mapped to the regions containing blast resistance genes Pi2 and Pia were chosen for Northern analysis after inoculation of plants with the blast fungus. Two of them, which code for a receptor-like kinase and a putative membrane channel protein, respectively, and were mapped to the Pi2 locus, were induced by rice blast infection as early as 4 h after inoculation. Transcription of another EST, which codes for a homolog of a putative human tumor suppressor and was mapped to the region containing Pia, was repressed after blast infection. These findings demonstrate that the candidate-gene approach is an efficient way of mapping resistance genes or resistance QTLs in rice.

Chromosome Mapping↗