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At least 127 records · Page 7Linked to original sources
PubMed1995

The maize GapC4 promoter confers anaerobic reporter gene expression and shows homology to the maize anthocyanin regulatory locus C1.

The cytosolic glyceraldehyde-3-phosphate dehydrogenase (GapC) gene family of maize is differentially expressed in response to anaerobic stress. While GapCl and GapC2 are downregulated, GapC3 and GapC4 are anaerobically induced. We have sequenced and analyzed a 3073 bp promoter fragment of GapC4. The promoter confers anaerobic induction of a reporter gene construct in a transient gene expression system in maize. Deletion analysis of the GapC4 promoter revealed a 270 bp long DNA region required for anaerobic induction. This region contains sequence motifs resembling the cis-acting sequences of the anaerobically induced maize Adh1 and Adh2 genes. Furthermore, the 3073 bp GapC4 promoter fragment displays homology to long terminal repeats of maize retrotransposons and to the 3' region of the maize anthocyanin regulatory locus C1.

Anaerobiosis↗
PubMed1996

Molecular analysis of the gene family of the signal recognition particle (SRP) RNA of tomato.

The sequence variants of the signal recognition particle (SRP) RNA gene family from four tomato cultivars have been isolated and characterized which indicated the existence of SRP RNA pseudogenes. Sequence analysis revealed two conserved sequence motifs in the upstream region, a TATA-like box and an upstream sequence element (USE), 'TCCCACATCG', both located at a conserved distance to the transcription start point. These elements are identical to the DNA-dependent RNA polymerase III (pol III)-specific promoters of U-rich small nuclear RNA (UsnRNA) genes of plants. Moreover, T-rich stretches are found at the 3' end of the coding regions of the SRP RNA genes which could act as typical pol III termination signals. These findings and recent results from site-directed mutation analysis of the SRP RNA genes from Arabidopsis thaliana indicate that, in contrast to mammalian systems, plant pol III SRP RNA genes are most probably regulated by external promoter elements. According to the identical promoter organization between plant U3-, U6snRNA, MRP-like RNA and SRP RNA genes, one can group these genes into the 'pol III(EXT)USE' subclass of externally regulated USE-dependent pol III genes.

Base Sequence↗
PubMed1994

mRNA accumulation and promoter activity of the gene coding for a hydroxyproline-rich glycoprotein in Oryza sativa.

The accumulation of the mRNA corresponding to the gene coding for a hydroxyproline-rich glycoprotein has been studies in rice. The patterns of gene expression obtained are similar to those observed in maize in regions rich in dividing cells such as the meristematic zones of roots. However, the gene does not seem to be induced by wounding as it is the case in maize. This effect is correlated with the absence of sequences present in the promoter of the maize gene and that have been described as responsible for ethylene induction on other plant systems. Instead, the promoter has a sequence that corresponds to abscisic acid-responsive elements and, in fact, HRGP mRNA levels can be two-fold increased in rice leaves by ABA. The genes coding for homologous proteins in two cereal species such as maize and rice appear, therefore, to have distinct mechanisms of gene regulation.

Abscisic Acid↗
PubMed1995

Evolution of the Group 1 late embryogenesis abundant (Lea) genes: analysis of the Lea B19 gene family in barley.

The highly conserved Group 1 late embryogenesis abundant (Lea) genes are present in the genome of most plants as a gene family. Family members are conserved along the entire coding region, especially within the extremely hydrophilic internal 20 amino acid motif, which may be repeated. Cloning of Lea Group 1 genes from barley resulted in the characterization of four family members named B19.1, B19.1b, B19.3 and B19.4 after the presence of this motif 1, 1, 3 and 4 times in each gene, respectively. We present here the results of comparative and evolutionary analyses of the barley Group 1 Lea gene family (B19). The most important findings resulting from this work are (1) the tandem clustering of B19.3 and B19.4, (2) the spatial conservation of putative regulatory elements between the four B19 gene promoters, (3) the determination of the relative 'age' of the gene family members and (4) the 'chimeric' nature of B19.3 and B19.4, reflecting a cross-over or gene-conversion event in their common ancestor. We also show evidence for the presence of one or two additional expressed B19 genes in the barley genome. Based on our results, we present a model for the evolution of the family in barley, including the 20 amino acid motif. Comparisons of the relatedness between the barley family and all other known Group 1 Lea genes using maximum parsimony (PAUP) analysis provide evidence for the time of divergence between the barley genes containing the internal motif as a single copy and as a repeat. The PAUP analyses also provide evidence for independent duplications of Group 1 genes containing the internal motif as a repeat in both monocots and dicots.

Base Sequence↗
PubMed1991

Sugar response element enhances wound response of potato proteinase inhibitor II promoter in transgenic tobacco.

The promoter region of the potato proteinase inhibitor II (PI-II) gene was studied to identify cis-acting regulatory sequences involved in sugar response using transgenic tobacco plants. The 5' control region covering an 892 nucleotide sequence upstream from the cap site and a 32 nucleotide untranslated region of the PI-II promoter was able to activate a reporter chloramphenicol acetyltransferase (cat) gene by wounding or by incubating in a sugar-free medium. This wound response was further enhanced by sugar. Hexoses, disaccharides, and some trisaccharides were strong inducers whereas pentoses, deoxy sugars, sugar acids, TCA cycle intermediates, amino acids, and other carbohydrates had little effect on the promoter activity. Deletion of the sequence between -892 and -573 abolished the wound response but not the sugar response. An additional 5' deletion to -453 removed the sugar inducibility. Locations of the cis-acting regulatory elements were further elucidated by 3' deletion analysis. Deletion of the downstream region from -520 did not affect the wound or sugar response of the promoter. However, 3' deletion mutant -574 was unable to respond to sugar but did respond weakly to wounding. Further deletion to -624 abolished both responses. Therefore, it can be concluded that a wound response element is located in between -624 and -574 and that the response is further enhanced by a sugar response element located in the sequence between -573 and -520.

Agrobacterium tumefaciens↗
PubMed1994

A 20 nucleotide upstream element is essential for the nopaline synthase (nos) promoter activity.

The nopaline synthase (nos) promoter is expressed in a wide range of plant cell types and regulated by various developmental and environmental factors. The nos upstream control region essential for this regulation was studied by means of synthetic oligomers using transient and stable transformation systems. Insertion of a 20 nucleotide sequence containing two hexamer motifs and a spacer region into deletion mutants lacking the upstream control region was essential for promoter activity. Mutation of one or more nucleotides of either hexamer sequence significantly altered the strength of expression of the nos promoter. Point mutations within the spacer region also strongly influenced promoter strength. Insertion of multiple copies of the 20 nucleotide sequence into the nonfunctional deletion mutants proportionally increased the promoter activity. These results suggest that this twenty nucleotide sequence is essential for the nos promoter to function. Substitution of the nos element with the ocs or 35S as-1 which contain similar hexamer motifs restored not only promoter activity but also responses to wounding, auxin, methyl jasmonate, and salicylic acid.

Amino Acid Oxidoreductases↗
PubMed1992

Natural genetic engineering in evolution.

The results of molecular genetics have frequently been difficult to explain by conventional evolutionary theory. New findings about the genetic conservation of protein structure and function across very broad taxonomic boundaries, the mosaic structure of genomes and genetic loci, and the molecular mechanisms of genetic change all point to a view of evolution as involving the rearrangement of basic genetic motifs. A more detailed examination of how living cells restructure their genomes reveals a wide variety of sophisticated biochemical systems responsive to elaborate regulatory networks. In some cases, we know that cells are able to accomplish extensive genome reorganization within one or a few cell generations. The emergence of bacterial antibiotic resistance is a contemporary example of evolutionary change; molecular analysis of this phenomenon has shown that it occurs by the addition rearrangement of resistance determinants and genetic mobility systems rather than by gradual modification of pre-existing cellular genomes. In addition, bacteria and other organisms have intricate repair systems to prevent genetic change by sporadic physicochemical damage or errors of the replication machinery. In their ensemble, these results show that living cells have (and use) the biochemical apparatus to evolve by a genetic engineering process. Future research will reveal how well the regulatory systems integrate genomic change into basic life processes during evolution.

Animals↗
PubMed1992

Phylogenetic evidence for multiple Alu source genes.

A member of the young PV Alu subfamily is detected in chimpanzee DNA showing that the PV subfamily is not specific to human DNA. This particular Alu is absent from the orthologous loci in both human and gorilla DNAs, indicating that PV subfamily members transposed within the chimpanzee lineage following the divergence of chimpanzee from both gorilla and human. These findings and previous reports describing the transpositional activity of other Alu sequences within the human, gorilla, and chimpanzee lineages provide phylogenetic evidence for the existence of multiple Alu source genes. Sequences surrounding this particular Alu resemble known transcriptional control elements associated with RNA polymerase III, suggesting a mechanism by which cis-acting elements might be acquired upon retrotransposition.

Animals↗
PubMed1993

Sequence evolution in and around the mitochondrial control region in birds.

By cloning and sequencing 3.4 kilobases of snow goose mtDNA we found that the ND5 gene is followed by the genes for cytochrome b, tRNA(Thr), tRNA(Pro), ND6, tRNA(Glu), the control region, tRNA(Phe), and srRNA. This order is identical to that of chicken, quail, and duck mtDNA but differs from that of mammals and a frog (Xenopus). The mean extent of difference due to base substitution between goose and chicken is generally closer to the same comparison between rat and mouse but less than that between human and cow. For one of the nine regions compared (tRNA(Glu)), the bird differences appear to be anomalous, possibly implicating altered functional constraints. Within the control region, several short sequences common to mammals are also conserved in the birds. Comparison of the goose control region with that of quail and chicken suggests that a sequence element with similarity to CSB-1 duplicated once prior to the divergence of goose and chicken and again on the lineage leading to chicken. Between goose (or duck) and chicken there are four times more transversions at the third positions of fourfold-degenerate codons in mitochondrial than in nuclear genes.

Amino Acid Sequence↗
PubMed1995

Redefinition of the coding sequence of the MXI1 gene and identification of a polymorphic repeat in the 3' non-coding region that allows the detection of loss of heterozygosity of chromosome 10q25 in glioblastomas.

The MXI1 gene encodes a protein interacting with Max, a regulatory factor of the Myc oncogene, and is located on chromosome 10q25, a region showing frequent loss of heterozygosity in malignant gliomas. We have reassessed the coding sequence of MXI1 and found that, at the 3' end, the open reading frame is 28 codons shorter than previously described. We have also found an AAAAC polymorphic repeat (two alleles, 45% heterozygosity) in the 3' non-coding region of the gene. Six anaplastic astrocytomas and nine glioblastomas, the most malignant form of glioma, were informative for this polymorphism. Loss of heterozygosity was demonstrated in all glioblastomas, but not in the remaining tumors.

Base Sequence↗
PubMed1993

Inter-ethnic polymorphism of the beta-globin gene locus control region (LCR) in sickle-cell anemia patients.

Sequence polymorphisms within the 5'HS2 segment of human locus control region is described among sickle cell anemia patients. Distinct polymorphic patterns of a simple sequence repeat are observed in strong linkage disequilibrium with each of the five major beta s haplotypes. Potential functional relevance of this polymorphic region in globin gene expression is discussed.

Algeria↗
PubMed1992

Riboflavin operon of Bacillus subtilis: unusual symmetric arrangement of the regulatory region.

Seventeen cis-dominant mutations leading to riboflavin overproduction in Bacillus subtilis were localized to the region between nucleotides +37 and +159 relative to the transcription initiation site of the riboflavin operon. This region displays an unusual structure for regulatory sequences. The main part of it represents clusters of A/T and G/C-rich sequences that symmetrically blank a short inverted repeat.

Bacillus subtilis↗
PubMed1993

Correlation between the size of the intergenic regulatory region, the status of cytosine methylation of rRNA genes and nucleolar expression in wheat.

A large number of wheat rRNA genes are methylated at all the CCGG sites that are present in the intergenic regions. A smaller number of rRNA genes are not methylated at one or more CCGG sites. A subset of genes was found unmethylated at a specific CCGG site just downstream of the array of 135 bp A repeats in the intergenic region. In all the genotypes studied, the rDNA loci with larger intergenic regions between their genes also possess a greater number of rRNA genes that are unmethylated at one or more CCGG sites in the intergenic regions than do the loci with shorter intergenic regions. In four genotypes (for which data were available), rDNA loci with longer intergenic regions had larger secondary constrictions on metaphase chromosomes, a measure of relative locus activity, than the loci with shorter intergenic regions. The results have been integrated into a model for the control of rDNA expression based on correlations between cytosine methylation patterns and the number of upstream 135 bp repeats in intergenic regions. According to this model the 135 bp repeats play a part in the control of gene activity by binding a protein(s) that is in limiting supply, thereby predisposing the neighbouring gene to become active preferentially.

Cell Nucleolus↗
PubMed1993

Cis-regulatory sequences leading to female-specific expression of yolk protein genes 1 and 2 in the fat body of Drosophila melanogaster.

The three yolk protein genes (yp) of Drosophila melanogaster are transcribed in a sex- and tissue-limited fashion. We have searched for cis-regulatory sequences in regions flanking yp1 and yp2 to identify the elements that confer female-specific expression in the fat body. One such 127 bp element has previously been identified in this region. We show here the existence of two additional regions which confer female fat body-specific expression on an Adh reporter gene and on the native yp2 gene, respectively. This suggests some redundancy in the regulation of expression of the yp genes. Computer searches for putative binding sites for the DSX protein, which regulates sex-specific expression of the yp genes, revealed several such sites in our constructs. However, the significance of these is unclear since many such sites also occur in genes which one would not expect to be regulated in a sex-specific manner (e.g. Adh, Actin 5C). We suggest that DSX acts in concert with other proteins to mediate sex- and tissue-specific expression of the yp genes.

Alcohol Dehydrogenase↗
PubMed1993

An abundant LINE-like element amplified in the genome of Lilium speciosum.

The genomes of Lilium species are very large, containing 30-40 million kilobase pairs of DNA. An abundant fragment of 3.5 kb was released by BamHI digestion of genomic DNA of Lilium speciosum. Analysis of 20 genomic clones containing sequences homologous to the fragment showed it to be part of a 4.45 kb dispersed repeat, which was named del2. Sequence analysis of one full element and regions of four others revealed del2 to be a non-LTR (long terminal repeat) retrotransposon. It is flanked by short direct repeats of from 4 to 13 bp and a run of adenines occurs at one end (the proposed 3' end), 63 bp downstream from a polyadenylation signal. A possible RNA polymerase II promoter similar to that found in Drosophila I and F group elements is present internally 30 bp downstream from the 5' end. Two degenerate open reading frames (ORFs) are present, the 5' ORF containing a gag-related cysteine motif, and the 3' ORF containing a different cysteine motif also found in most non-LTR retrotransposons. The 3' ORF also has regions with homology to reverse transcriptase sequences, which are most similar to those in Cin4 of maize, the L1 LINE elements of humans and mice and the R2 ribosomal DNA inserts of insects. The majority of del2 elements occur as the full 4.45 kb element. They account for an estimated 4% of the L. speciosum genome and are present in approximately 250,000 copies. del2-related sequences were also detected in 12 other monocot species.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1993

Functional in vivo analyses of the 3' flanking sequences of the Chlamydomonas chloroplast rbcL and psaB genes.

Possible roles of untranslated sequences at the 3' ends of chloroplast genes, which include inverted repeat elements, were investigated in Chlamydomonas reinhardtii in vivo. Chlamydomonas chloroplast rbcL or psaB 3' flanking regions were coupled in various arrangements 3' to a chimeric gene consisting of a Chlamydomonas chloroplast atpB promoter sequence fused 5' to the Escherichia coli uidA (GUS) structural gene. These genes were introduced into the Chlamydomonas chloroplast genome at the same location by homologous recombination following microprojectile bombardment. Transformants harboring chimeric GUS genes fused to rbcL or psaB gene 3' inverted repeat sequences in their normal forward orientations accumulated GUS transcripts of a single size, whereas GUS transcripts of heterogenous sizes accumulated in transformants harboring the same gene lacking an inverted repeat sequence at its 3' end. Thus, the 3' flanking regions of the rbcL and psaB genes can define the location of the 3' terminus of a transcript in vivo. In chloroplast transformants harboring chimeric GUS genes fused to multiple inverted repeat sequences in their normal forward orientations, only GUS transcripts accumulated that were terminated by the first inverted repeat sequence. The latter data suggest that the 3' ends of these RNAs are the products of either transcription termination or endonucleolytic cleavage. Analyses of GUS transcripts in transformants harboring GUS genes terminated by rbcL or psaB gene 3' flanking regions in reversed orientations indicate that transcript 3' end formation in vivo requires nucleotide sequences located outside the inverted repeat elements. Inasmuch as decay rates of GUS transcripts were found to be independent of the presence of a 3' inverted repeat sequence, RNA stabilization does not appear to be a major in vivo function of these elements in the Chlamydomonas chloroplast transcripts studied.

Animals↗
PubMed1993

Promoter analysis of the PHO81 gene encoding a 134 kDa protein bearing ankyrin repeats in the phosphatase regulon of Saccharomyces cerevisiae.

The PHO81 gene encoding one of the regulators of the phosphatase regulon in Saccharomyces cerevisiae was mapped 9.8 centimorgans distal from the ser2 locus on the right arm of chromosome VII. Determination of the nucleotide sequence of cloned PHO81 DNA revealed a 3537 bp open reading frame encoding a 134 kDa protein. This protein has six repeats of a 33-amino acid sequence homologous to the ankyrin repeat and an asparagine-rich region. Transcription of PHO81 is activated by Pho4 protein in cooperation with Pho2 (i.e., Bas2/Grf10) protein under the influence of the inorganic phosphate (Pi) concentration in the medium, through the PHO regulatory system. Major transcription initiation sites of PHO81, determined by primer extension analysis, are at nucleotide positions -66 and -65 relative to the ATG codon. Deletion analysis showed that a 95 bp region from nucleotide position -385 to -291 is essential for response to the Pi signals. Purified Pho4 protein protected a 19 bp region (positions -350 to -332) in the 95 bp fragment from DNase I digestion in vitro and the protected region includes the core sequence 5'-CACGTG-3', which is also observed in other genes of phosphate metabolism.

Acid Phosphatase↗