scholarly journals An open reading frame in intron seven of the sea urchin DNA-methyltransferase gene codes for a functional AP1 endonuclease

2002 ◽  
Vol 365 (3) ◽  
pp. 833-840 ◽  
Author(s):  
Anna Valentina CIOFFI ◽  
Diana FERRARA ◽  
Maria Vittoria CUBELLIS ◽  
Francesco ANIELLO ◽  
Marcella CORRADO ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Dna Methyltransferase ◽  
Developmental Stages ◽  
Genome Structure ◽  
Three Dimensional ◽  
Paracentrotus Lividus ◽  
Open Reading Frame ◽  
Dimensional Structure ◽  
Cdna Clones ◽  
Reading Frame

Analysis of the genome structure of the Paracentrotus lividus (sea urchin) DNA methyltransferase (DNA MTase) gene showed the presence of an open reading frame, named METEX, in intron 7 of the gene. METEX expression is developmentally regulated, showing no correlation with DNA MTase expression. In fact, DNA MTase transcripts are present at high concentrations in the early developmental stages, while METEX is expressed at late stages of development. Two METEX cDNA clones (Met1 and Met2) that are different in the 3′ end have been isolated in a cDNA library screening. The putative translated protein from Met2 cDNA clone showed similarity with Escherichia coli endonuclease III on the basis of sequence and predictive three-dimensional structure. The protein, overexpressed in E. coli and purified, had functional properties similar to the endonuclease specific for apurinic/apyrimidinic (AP) sites on the basis of the lyase activity. Therefore the open reading frame, present in intron 7 of the P. lividus DNA MTase gene, codes for a functional AP endonuclease designated SuAP1.

scholarly journals Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungusEpichloë festucae

2018 ◽  
Author(s):  
David J Winter ◽  
Austen RD Ganley ◽  
Carolyn A Young ◽  
Ivan Liachko ◽  
Christopher L Schardl ◽  
...  
Keyword(s):  
Genome Structure ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
In Planta ◽  
Repeat Elements ◽  
Symbiotic Relationships ◽  
3D Genome ◽  
Transcriptional Changes

AbstractStructural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organization influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus,Epichloë festucae. Coupling it with RNAseq and HiC data, we investigate how the structure of the genome contributes to the suite of transcriptional changes that anEpichloëspecies needs to maintain symbiotic relationships with its grass host. Our results reveal a unique “patchwork” genome, in which repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences. In contrast to other species, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.

Pax-6, a murine paired box gene, is expressed in the developing CNS

Development ◽  
1991 ◽  
Vol 113 (4) ◽  
pp. 1435-1449 ◽  
Author(s):  
C. Walther ◽  
P. Gruss
Keyword(s):  
Amino Acids ◽  
Neural Tube ◽  
Multigene Family ◽  
Ventricular Zone ◽  
Open Reading Frame ◽  
Cdna Clones ◽  
Coding Region ◽  
Paired Domain ◽  
Reading Frame ◽  
Pax Genes

A multigene family of paired-box-containing genes (Pax genes) has been identified in the mouse. In this report, we describe the expression pattern of Pax-6 during embryogenesis and the isolation of cDNA clones spanning the entire coding region. The Pax-6 protein consists of 422 amino acids as deduced from the longest open reading frame and contains, in addition to the paired domain, a paired-type homeodomain. Beginning with day 8 of gestation, Pax-6 is expressed in discrete regions of the forebrain and the hindbrain. In the neural tube, expression is mainly confined to mitotic active cells in the ventral ventricular zone along the entire anteroposterior axis starting at day 8.5 of development. Pax-6 is also expressed in the developing eye, the pituitary and the nasal epithelium.

scholarly journals Identification of a positive regulator of the cell cycle ubiquitin-conjugating enzyme Cdc34 (Ubc3).

1996 ◽  
Vol 16 (2) ◽  
pp. 677-684 ◽  
Author(s):  
J A Prendergast ◽  
C Ptak ◽  
D Kornitzer ◽  
C N Steussy ◽  
R Hodgins ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Amino Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Temperature Sensitive ◽  
Reading Frame ◽  
Positive Regulator ◽  
Morphological Defects ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

The Cdc34 (Ubc3) ubiquitin-conjugating enzyme from Saccharomyces cerevisiae plays an essential role in the progression of cells from the G1 to S phase of the cell division cycle. Using a high-copy suppression strategy, we have identified a yeast gene (UBS1) whose elevated expression suppresses the conditional cell cycle defects associated with cdc34 mutations. The UBS1 gene encodes a 32.2-kDa protein of previously unknown function and is identical in sequence to a genomic open reading frame on chromosome II (GenBank accession number Z36034). Several lines of evidence described here indicate that Ubs1 functions as a general positive regulator of Cdc34 activity. First, overexpression of UBS1 suppresses not only the cell proliferation and morphological defects associated with cdc34 mutants but also the inability of cdc34 mutant cells to degrade the general amino acid biosynthesis transcriptional regulator, Gcn4. Second, deletion of the UBS1 gene profoundly accentuates the cell cycle defect when placed in combination with a cdc34 temperature-sensitive allele. Finally, a comparison of the Ubs1 and Cdc34 polypeptide sequences reveals two noncontiguous regions of similarity, which, when projected onto the three-dimensional structure of a ubiquitin-conjugating enzyme, define a single region situated on its surface. While cdc34 mutations corresponding to substitutions outside this region are suppressed by UBS1 overexpression, Ubs1 fails to suppress amino acid substitutions made within this region. Taken together with other findings, the allele specificity exhibited by UBS1 expression suggests that Ubs1 regulates Cdc34 by interaction or modification.

scholarly journals Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation

2009 ◽  
Vol 83 (20) ◽  
pp. 10719-10736 ◽  
Author(s):  
Corinne Rancurel ◽  
Mahvash Khosravi ◽  
A. Keith Dunker ◽  
Pedro R. Romero ◽  
David Karlin
Keyword(s):  
De Novo ◽  
Three Dimensional ◽  
Structural Disorder ◽  
Dimensional Structure ◽  
Overlapping Genes ◽  
Reading Frame ◽  
Sequence Composition ◽  
Overlapping Reading Frames ◽  
Almost All ◽  
Novel Protein

ABSTRACT It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called “overprinting.” To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition globally biased toward disorder-promoting amino acids and are predicted to contain significantly more structural disorder than nonoverlapping proteins. By analyzing the phylogenetic distribution of overlapping proteins, we were able to confirm that 17 of these had been created de novo and to study them individually. Most proteins created de novo are orphans (i.e., restricted to one species or genus). Almost all are accessory proteins that play a role in viral pathogenicity or spread, rather than proteins central to viral replication or structure. Most proteins created de novo are predicted to be fully disordered and have a highly unusual sequence composition. This suggests that some viral overlapping reading frames encoding hypothetical proteins with highly biased composition, often discarded as noncoding, might in fact encode proteins. Some proteins created de novo are predicted to be ordered, however, and whenever a three-dimensional structure of such a protein has been solved, it corresponds to a fold previously unobserved, suggesting that the study of these proteins could enhance our knowledge of protein space.

scholarly journals Phenylalanine ammonia-lyase (PAL) from tobacco (Nicotiana tabacum): characterization of the four tobacco PAL genes and active heterotetrameric enzymes1

2009 ◽  
Vol 424 (2) ◽  
pp. 233-242 ◽  
Author(s):  
Angelika I. Reichert ◽  
Xian-Zhi He ◽  
Richard A. Dixon
Keyword(s):  
Nicotiana Tabacum ◽  
Phenylalanine Ammonia Lyase ◽  
Consensus Sequence ◽  
Three Dimensional ◽  
Pcr Amplification ◽  
Dimensional Structure ◽  
Kinetic Properties ◽  
Cdna Clones ◽  
Phenylpropanoid Biosynthesis ◽  
The Individual

PAL (L-phenylalanine ammonia-lyase), the first enzyme of phenylpropanoid biosynthesis, is often encoded by multigene families in plants. A PCR-based approach was used to isolate cDNA clones corresponding to the four PAL genes of tobacco (Nicotiana tabacum). By careful comparison of cDNA and genomic clones, a new PAL gene (PAL4) was defined. PCR amplification of PAL sequences from cDNA led to the generation of chimaeric clones between PAL1 and PAL4, and incorrect annotation of PAL4 ESTs (expressed sequence tags) as PAL1 in the EST database has given rise to a randomly shuffled tentative consensus sequence. The PAL2 previously described in the literature was shown, by domain swapping experiments with PAL1, to possess a single nucleotide substitution leading to an inactive enzyme. The altered amino acid resulting from this substitution maps to the base of the active site pocket in the three-dimensional structure of PAL. The inactive PAL2 allele could not be recovered from 13 different tobacco cultivars examined. PALs 1–4 were co-expressed in multiple plant organs, and were also co-induced following exposure of cell cultures to yeast elicitor or methyl jasmonate. All four tobacco PAL proteins expressed in Escherichia coli displayed normal Michaelis–Menten kinetics, with Km values between 36 and 60 μM. Co-expression of different PAL proteins in E. coli resulted in formation of heterotetramers, which possessed kinetic properties within the same range as those of the individual homotetramers. The potential physiological function of heterotetrameric PAL forms is discussed.

scholarly journals A highly conserved mouse gene with a propensity to form pseudogenes in mammals.

1988 ◽  
Vol 8 (7) ◽  
pp. 2797-2803 ◽  
Author(s):  
D L Heller ◽  
K M Gianola ◽  
L A Leinwand
Keyword(s):  
Dna Sequence ◽  
Cdna Clone ◽  
Restriction Analysis ◽  
In Vitro Transcription ◽  
Open Reading Frame ◽  
Cdna Clones ◽  
Reading Frame ◽  
Mouse Cdna ◽  
Processed Pseudogenes

A mouse cDNA clone corresponding to an abundantly transcribed poly(A)+ mRNA was found to be represented by 200 copies in mammalian genomes. To understand the origin and nature of this sequence family, we studied two genomic members and two cDNA clones from mouse liver. The DNA sequence of the coding strand of a full-length cDNA clone was shown to have an open reading frame capable of encoding a 25-kilodalton polypeptide that has not been previously described. In vitro transcription-translation experiments verified the presence of an open reading frame encoding a protein of the predicted size. Restriction analysis of genomic DNA and DNA sequence analysis of genomic clones indicated that many of the 200 members of this family represent processed pseudogenes, with one or a small number of active structural genes. The vast majority of the genomic copies are heterogeneous in length, truncated at their 5' ends with respect to the mRNA, and do not appear to have intervening sequences. Two distinct genomic members of this family were sequenced and found to represent incomplete copies of the mRNA. Both are 5' truncated at slightly different points with respect to the mRNA. Both pseudogenes have multiple base changes, insertions, and deletions relative to the mRNA, and one of them encodes the poly(A) tail of the mRNA. The expression of this gene family is highest in rapidly dividing cells such as early mouse embryos and testis, but was seen in all tissues tested. This gene shows extremely high sequence conservation, extending to chicken, amphibian, and nematode genomes. Surprisingly, the gene appears to exist in only one copy in these organisms.

scholarly journals ANTIGENS IN EGGS AND DEVELOPMENTAL STAGES OF THE SEA URCHIN

1961 ◽  
Vol 9 (1) ◽  
pp. 93-104 ◽  
Author(s):  
Jane Couffer-Kaltenbach ◽  
Peter Perlmann
Keyword(s):  
Physicochemical Properties ◽  
Electrophoretic Mobility ◽  
Sea Urchin ◽  
Diffusion Coefficients ◽  
Developmental Stages ◽  
Paracentrotus Lividus ◽  
Serial Dilution ◽  
Gradual Transition ◽  
Migration Rates

A number of antigens in unfertilized eggs and embryos of the sea urchin Paracentrotus lividus were characterized with respect to both immunological and physicochemical properties. Experiments involved single diffusion in agar (Oudin technique) combined with mutual dilution, serial dilution, and heating of antigenic extracts, as well as immunoelectrophoresis with normal and heated extracts and agar electrophoresis followed by staining of the antigenic spots with protein specific dyes. The gradual transition in migration rates of bands of precipitates in Oudin tubes following mutual dilution of either extracts or antisera allowed the identification of 6 immunologically identical antigens in eggs and embryonic stages. Similarities with respect to diffusion coefficients, sensitivity to heat, electrophoretic mobility, and reaction to protein specific dyes indicated that the antigens in extracts of eggs and various developmental stages also had certain physicochemical properties in common. Such knowledge is of importance for an understanding of antigenic changes occurring during ontogenesis.

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