The 190 kDa centrosome-associated protein of Drosophila melanogaster contains four zinc finger motifs and binds to specific sites on polytene chromosomes

STP1 is an unessential yeast gene involved in the removal of intervening sequences from some, but not all, families of intervening sequence-containing pre-tRNAs. Previously, we proposed that STP1 might encode a product that generates pre-tRNA conformations efficiently recognized by tRNA-splicing endonuclease. To test the predictions of this model, we have undertaken a molecular analysis of the STP1 gene and its products. The STP1 locus is located on chromosome IV close to at least two other genes involved in RNA splicing: PRP3 and SPP41. The STP1 open reading frame (ORF) could encode a peptide of 64,827 Da; however, inspection of putative transcriptional and translational regulatory signals and mapping of the 5' ends of mRNA provide evidence that translation of the STP1 ORF usually initiates at a second AUG to generate a protein of 58,081 Da. The STP1 ORF contains three putative zinc fingers. The first of these closely resembles both the DNA transcription factor consensus and the Xenopus laevis p43 RNA-binding protein consensus. The third motif more closely resembles the fingers found in spliceosomal proteins. Employing antisera to the endogenous STP1 protein and to STP1-LacZ fusion proteins, we show that the STP1 protein is localized to nuclei. The presence of zinc finger motifs and the nuclear location of the STP1 protein support the model that this gene product is involved directly in pre-tRNA splicing.

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DNA Supercoiling Factor Localizes to Puffs on Polytene Chromosomes in Drosophila melanogaster

Molecular and Cellular Biology ◽

10.1128/mcb.18.11.6737 ◽

1998 ◽

Vol 18 (11) ◽

pp. 6737-6744 ◽

Cited By ~ 18

Author(s):

Masatomo Kobayashi ◽

Noriko Aita ◽

Shigeo Hayashi ◽

Kohichi Okada ◽

Tsutomu Ohta ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Topoisomerase Ii ◽

Polytene Chromosomes ◽

Posterior Part ◽

Dna Supercoiling ◽

Northern Analysis ◽

Nuclear Fraction ◽

Mitotic Chromosomes ◽

Reading Frame

ABSTRACT DNA supercoiling factor (SCF) was first identified in silkworm as a protein that generates negative supercoils in DNA in conjunction with eukaryotic topoisomerase II. To analyze the in vivo role of the factor, we cloned a cDNA encoding Drosophila melanogaster SCF. Northern analysis revealed 1.6- and 1.8-kb mRNAs throughout development. The longer mRNA contains an open reading frame that shares homology with mouse reticulocalbin whereas the shorter one encodes a truncated version lacking the N-terminal signal peptide-like sequence. An antibody against SCF detected a 45-kDa protein in the cytoplasmic fraction and a 30-kDa protein in the nuclear fraction of embryonic extracts. Immunoprecipitation suggests that the 30-kDa protein interacts with topoisomerase II in the nucleus, and hence that it is a functional form of SCF. Immunostaining of blastoderm embryos showed that SCF is present in nuclei during interphase but is excluded from mitotic chromosomes. In larvae, the antibody stained the nuclei of several tissues including a posterior part of the salivary gland. This latter staining was associated with natural or ecdysteroid-induced puffs on polytene chromosomes. Upon heat treatment of larvae, the staining on the endogenous puffs disappeared, and strong staining appeared on heat shock puffs. These results implicate SCF in gene expression.

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Analysis of Two Cosmid Clones from Chromosome 4 of Drosophila melanogaster Reveals Two New Genes Amid an Unusual Arrangement of Repeated Sequences

Genome Research ◽

10.1101/gr.9.2.137 ◽

1999 ◽

Vol 9 (2) ◽

pp. 137-149 ◽

Cited By ~ 1

Author(s):

John Locke ◽

Lynn Podemski ◽

Ken Roy ◽

David Pilgrim ◽

Ross Hodgetts

Keyword(s):

Drosophila Melanogaster ◽

Dna Sequences ◽

Polytene Chromosomes ◽

Mobile Element ◽

The Other ◽

P Element ◽

Matrix Analysis ◽

Predicted Amino Acid Sequence ◽

Chromosome 4 ◽

New Genes

Chromosome 4 from Drosophila melanogaster has several unusual features that distinguish it from the other chromosomes. These include a diffuse appearance in salivary gland polytene chromosomes, an absence of recombination, and the variegated expression of P-element transgenes. As part of a larger project to understand these properties, we are assembling a physical map of this chromosome. Here we report the sequence of two cosmids representing ∼5% of the polytenized region. Both cosmid clones contain numerous repeated DNA sequences, as identified by cross hybridization with labeled genomic DNA, BLAST searches, and dot matrix analysis, which are positioned between and within the transcribed sequences. The repetitive sequences include three copies of the mobile element Hoppel, one copy of the mobile element HB, and 18 DINE repeats. DINE is a novel, short repeated sequence dispersed throughout both cosmid sequences. One cosmid includes the previously described cubitus interruptus(ci) gene and two new genes: that a gene with a predicted amino acid sequence similar to ribosomal protein S3a which is consistent with the Minute(4)101 locus thought to be in the region, and a novel member of the protein family that includes plexin and met–hepatocyte growth factor receptor. The other cosmid contains only the two short 5′-most exons from thezinc-finger-homolog-2 (zfh-2) gene. This is the first extensive sequence analysis of noncoding DNA from chromosome 4. The distribution of the various repeats suggests its organization is similar to the β-heterochromatic regions near the base of the major chromosome arms. Such a pattern may account for the diffuse banding of the polytene chromosome 4 and the variegation of many P-element transgenes on the chromosome.

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A stage-specific open reading frame from three-day old adult worms ofTrichinella spiralisencodes zinc-finger motifs

Parasite ◽

10.1051/parasite/2005122151 ◽

2005 ◽

Vol 12 (2) ◽

pp. 151-157 ◽

Cited By ~ 7

Author(s):

X.P. Zhu ◽

P. Garcia-Reyna ◽

B.Q. Fu ◽

J. Yang ◽

C.V. Li ◽

...

Keyword(s):

Zinc Finger ◽

Open Reading Frame ◽

Reading Frame ◽

Zinc Finger Motifs ◽

Old Adult

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STP1, a gene involved in pre-tRNA processing, encodes a nuclear protein containing zinc finger motifs.

Molecular and Cellular Biology ◽

10.1128/mcb.12.6.2633 ◽

1992 ◽

Vol 12 (6) ◽

pp. 2633-2643 ◽

Cited By ~ 10

Author(s):

S S Wang ◽

D R Stanford ◽

C D Silvers ◽

A K Hopper

Keyword(s):

Zinc Finger ◽

Rna Splicing ◽

Rna Binding ◽

Zinc Fingers ◽

Yeast Gene ◽

Reading Frame ◽

Trna Splicing ◽

Intervening Sequences ◽

Zinc Finger Motifs ◽

Nuclear Location

STP1 is an unessential yeast gene involved in the removal of intervening sequences from some, but not all, families of intervening sequence-containing pre-tRNAs. Previously, we proposed that STP1 might encode a product that generates pre-tRNA conformations efficiently recognized by tRNA-splicing endonuclease. To test the predictions of this model, we have undertaken a molecular analysis of the STP1 gene and its products. The STP1 locus is located on chromosome IV close to at least two other genes involved in RNA splicing: PRP3 and SPP41. The STP1 open reading frame (ORF) could encode a peptide of 64,827 Da; however, inspection of putative transcriptional and translational regulatory signals and mapping of the 5' ends of mRNA provide evidence that translation of the STP1 ORF usually initiates at a second AUG to generate a protein of 58,081 Da. The STP1 ORF contains three putative zinc fingers. The first of these closely resembles both the DNA transcription factor consensus and the Xenopus laevis p43 RNA-binding protein consensus. The third motif more closely resembles the fingers found in spliceosomal proteins. Employing antisera to the endogenous STP1 protein and to STP1-LacZ fusion proteins, we show that the STP1 protein is localized to nuclei. The presence of zinc finger motifs and the nuclear location of the STP1 protein support the model that this gene product is involved directly in pre-tRNA splicing.

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The Only Function of Grauzone Required for Drosophila Oocyte Meiosis Is Transcriptional Activation of the cortex Gene

Genetics ◽

10.1093/genetics/155.4.1831 ◽

2000 ◽

Vol 155 (4) ◽

pp. 1831-1839

Author(s):

Emily Harms ◽

Tehyen Chu ◽

Gwénola Henrion ◽

Sidney Strickland

Keyword(s):

Zinc Finger ◽

Transcriptional Activation ◽

Single Amino Acid ◽

Primary Role ◽

Extra Copy ◽

Oocyte Meiosis ◽

Zinc Finger Motifs ◽

High Level ◽

Transcriptional Pathway

Abstract The grauzone and cortex genes are required for the completion of meiosis in Drosophila oocytes. The grauzone gene encodes a C2H2-type zinc-finger transcription factor that binds to the cortex promoter and is necessary for high-level activation of cortex transcription. Here we define the region of the cortex promoter to which Grauzone binds and show that the binding occurs through the C-terminal, zinc-finger-rich region of the protein. Mutations in two out of the five grauzone alleles result in single amino acid changes within different zinc-finger motifs. Both of these mutations result in the inability of Grauzone to bind DNA effectively. To determine the mechanism by which Grauzone regulates meiosis, transgenic flies were produced with an extra copy of the cortex gene in homozygous grauzone females. This transgene rescued the meiosis arrest of embryos from these mutants and allowed their complete development, indicating that activation of cortex transcription is the primary role of Grauzone during Drosophila oogenesis. These experiments further define a new transcriptional pathway that controls the meiotic cell cycle in Drosophila oocytes.

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Chromosomal Distribution of Transposable Elements in Drosophila melanogaster Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number

Genetics ◽

10.1093/genetics/144.1.197 ◽

1996 ◽

Vol 144 (1) ◽

pp. 197-204

Author(s):

Christine Hoogland ◽

Christian Biémont

Keyword(s):

Drosophila Melanogaster ◽

Transposable Elements ◽

Dna Content ◽

Recombination Rate ◽

Alternative Hypothesis ◽

Insertion Site ◽

Polytene Chromosomes ◽

Negative Relationship ◽

Site Occupancy ◽

Site Number

Abstract Data of insertion site localization and site occupancy frequency of P, hobo, I, copia, mdg1, mdg3, 412, 297, and roo transposable elements (TEs) on the polytene chromosomes of Drosophila melanogaster were extracted from the literature. We show that TE insertion site number per chromosomal division was significantly correlated with the amount of DNA. The insertion site number weighted by DNA content was not correlated with recombination rate for all TEs except hobo, for which a positive correlation was detected. No global tendency emerged in the relationship between TE site occupancy frequency, weighted by DNA content, and recombination rate; a strong negative correlation was, however, found for the 3L arm. A possible dominant deleterious effect of chromosomal rearrangements due to recombination between TE insertions is thus not the main factor explaining the dynamics of TEs, since this hypothesis implies a negative relationship between recombination rate and both TE insertion site number and site occupancy frequency. The alternative hypothesis of selection against deleterious effects of insertional mutations is discussed.

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Genetic Analysis of the Drosophila 63F Early Puff: Characterization of Mutations in E63-1 and maggie, a Putative Tom22

Genetics ◽

10.1093/genetics/156.1.229 ◽

2000 ◽

Vol 156 (1) ◽

pp. 229-244

Author(s):

Martina Vaskova ◽

A M Bentley ◽

Samantha Marshall ◽

Pamela Reid ◽

Carl S Thummel ◽

...

Keyword(s):

Salivary Gland ◽

Genetic Analysis ◽

Polytene Chromosomes ◽

Reading Frame ◽

Protein Levels ◽

Ef Hand ◽

Larval Salivary Gland ◽

Complementation Groups ◽

Inducible Genes ◽

Early Puff

Abstract The 63F early puff in the larval salivary gland polytene chromosomes contains the divergently transcribed E63-1 and E63-2 ecdysone-inducible genes. E63-1 encodes a member of the EF-hand family of Ca2+-binding proteins, while E63-2 has no apparent open reading frame. To understand the functions of the E63 genes, we have determined the temporal and spatial patterns of E63-1 protein expression, as well as undertaken a genetic analysis of the 63F puff. We show that E63-1 is expressed in many embryonic and larval tissues, but the third-instar larval salivary gland is the only tissue where increases in protein levels correlate with increases in ecdysone titer. Furthermore, the subcellular distribution of E63-1 protein changes dynamically in the salivary glands at the onset of metamorphosis. E63-1 and E63-2 null mutations, however, have no effect on development or fertility. We have characterized 40 kb of the 63F region, defined as the interval between Ubi-p and E63-2, and have identified three lethal complementation groups that correspond to the dSc-2, ida, and mge genes. We show that mge mutations lead to first-instar larval lethality and that Mge protein is similar to the Tom22 mitochondrial import proteins of fungi, suggesting that it has a role in mitochondrial function.

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