scholarly journals Germ line and embryonic expression of Fex, a member of the Drosophila F-element retrotransposon family, is mediated by an internal cis-regulatory control region.

1996 ◽  
Vol 16 (6) ◽  
pp. 2998-3007 ◽  
Author(s):  
B Kerber ◽  
S Fellert ◽  
H Taubert ◽  
M Hoch
Keyword(s):  
Germ Line ◽  
Expression Patterns ◽  
Regulatory Region ◽  
Open Reading Frames ◽  
Regulatory Control ◽  
Nucleic Acid Binding ◽  
Coding Region ◽  
Reading Frame ◽  
Cis Acting ◽  
Retrotransposon Family

The F elements of Drosophila melanogaster belong to the superfamily of long interspersed nucleotide element retrotransposons. To date, F-element transcription has not been detected in flies. Here we describe the isolation of a member of the F-element family, termed Fex, which is transcribed in specific cells of the female and male germ lines and in various tissues during embryogenesis of D. melanogaster. Sequence analysis revealed that this element contains two complete open reading frames coding for a putative nucleic acid-binding protein and a putative reverse transcriptase. Functional analysis of the 5' region, using germ line transformation of Fex-lacZ reporter gene constructs, demonstrates that major aspects of tissue-specific Fex expression are controlled by internal cis-acting elements that lie in the putative coding region of open reading frame 1. These sequences mediate dynamic gene expression in eight expression domains during embryonic and germ line development. The capacity of the cis-regulatory region of the Fex element to mediate such complex expression patterns is unique among members of the long interspersed nucleotide element superfamily of retrotransposons and is reminiscent of regulatory regions of developmental control genes.

IDENTIFICATION, SEQUENCE AND EXPRESSION OF A CRUSTACEAN CARDIOACTIVE PEPTIDE (CCAP) GENE IN THE MOTHMANDUCA SEXTA

2001 ◽  
Vol 204 (16) ◽  
pp. 2803-2816 ◽  
Author(s):  
P. K. LOI ◽  
S. A. EMMAL ◽  
Y. PARK ◽  
N. J. TUBLITZ
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Gene Structure ◽  
Expression Patterns ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Genome Database ◽  
Reading Frame ◽  
Crustacean Cardioactive Peptide ◽  
Embryonic Life

SUMMARYThe crustacean cardioactive peptide (CCAP) gene was isolated from the tobacco hawkmoth Manduca sexta. The gene has an open reading frame of 125 amino acid residues containing a single, complete copy of CCAP. Analysis of the gene structure revealed three introns interrupting the coding region. A comparison of the M. sexta CCAP gene with the Drosophila melanogaster genome database reveals significant similarities in sequence and gene structure.The spatial and temporal expression patterns of the CCAP gene in the M. sexta central nervous system were determined in all major post-embryonic stages using in situ hybridization techniques. The CCAP gene is expressed in a total of 116 neurons in the post-embryonic M. sextacentral nervous system. Nine pairs of cells are observed in the brain, 4.5 pairs in the subesophageal ganglion, three pairs in each thoracic ganglion(T1-T3), three pairs in the first abdominal ganglion (A1), five pairs each in the second to sixth abdominal ganglia (A2-A6) and 7.5 pairs in the terminal ganglion. The CCAP gene is expressed in every ganglion in each post-embryonic stage, except in the thoracic ganglia of first- and second-instar larvae. The number of cells expressing the CCAP gene varies during post-embryonic life,starting at 52 cells in the first instar and reaching a maximum of 116 shortly after pupation. One set of thoracic neurons expressing CCAP mRNA shows unusual variability in expression levels immediately prior to larval ecdysis. Using previously published CCAP immunocytochemical data, it was determined that 91 of 95 CCAP-immunopositive neurons in the M. sexta central nervous system also express the M. sexta CCAP gene, indicating that there is likely to be only a single CCAP gene in M. sexta.

scholarly journals An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA

2019 ◽  
Vol 7 (1) ◽  
pp. 9 ◽  
Author(s):  
Dae-Eun Cheong ◽  
So-Youn Park ◽  
Ho-Dong Lim ◽  
Geun-Joong Kim
Keyword(s):  
Gene Expression ◽  
Regulatory Element ◽  
Expression System ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Single Element ◽  
Reading Frame ◽  
Cis Acting ◽  
Dna Libraries ◽  
Expression Module

Many integrated gene clusters beyond a single genetic element are commonly trapped as the result of promoter traps in (meta)genomic DNA libraries. Generally, a single element, which is mainly the promoter, is deduced from the resulting gene clusters and employed to construct a new expression vector. However, expression patterns of target proteins under the incorporated promoter are often inconsistent with those shown in clones harboring plasmids with gene clusters. These results suggest that the integrated set of gene clusters with diverse cis- and trans-acting elements is evolutionarily tuned as a complete set for gene expression, and is an expression module with all the components for the expression of a nested open reading frame (ORF). This possibility is further supported by truncation and/or serial deletion analysis of this module in which the expression of the nested ORF is highly fluctuated or reduced frequently, despite being supported by plentiful cis-acting elements in the spanning regions around the ORF such as the promoter, ribosome binding site (RBS), terminator, and 3′-/5′-UTRs for gene expression. Here, we examined whether an innate module with a naturally overexpressed gene could be considered as a scaffold for an expression system. For a proof-of-principle study, we mined a complete expression module with an innately overexpressed ORF in E. coli from a metagenomics DNA library, and incorporated it into a vector that had no regulatory element for expressing the insert. We obtained successful expression of several inserts such as MBP, GFPuv, β-glucosidase, and esterase using this simple construct without tuning and codon optimization of the target insert.

Evolutionary conservation of homeodomain-binding sites and other sequences upstream and within the major transcription unit of the Drosophila segmentation gene engrailed

1989 ◽  
Vol 9 (10) ◽  
pp. 4304-4311
Author(s):  
J A Kassis ◽  
C Desplan ◽  
D K Wright ◽  
P H O'Farrell
Keyword(s):  
Binding Sites ◽  
Regulatory Region ◽  
Divergence Time ◽  
Evolutionary Conservation ◽  
Transcription Unit ◽  
Regulatory Proteins ◽  
Coding Region ◽  
Cis Acting ◽  
Perfect Sequence ◽  
Development Proceeds

The engrailed (en) gene functions throughout Drosophila development and is expressed in a succession of intricate spatial patterns as development proceeds. Normal en function relies on an extremely large cis-acting regulatory region (70 kilobases). We are using evolutionary conservation to help identify en sequences important in regulating patterned expression. Sequence comparison of 2.6 kilobases upstream of the en coding region of D. melanogaster and D. virilis (estimated divergence time, 60 million years) showed that 30% of this DNA occurs in islands of near perfect sequence conservation. One of these conserved islands contains binding sites for homeodomain-containing proteins. It has been shown genetically that homeodomain-containing proteins regulate en expression. Our data suggested that this regulation may be direct. The remaining conserved islands may contain binding sites for other regulatory proteins.

Identification of a cis-acting sequence required for germ line-specific splicing of the P element ORF2-ORF3 intron

1991 ◽  
Vol 11 (3) ◽  
pp. 1538-1546
Author(s):  
A C Chain ◽  
S Zollman ◽  
J C Tseng ◽  
F A Laski
Keyword(s):  
Drosophila Melanogaster ◽  
Splice Site ◽  
Germ Line ◽  
Somatic Cells ◽  
Regulatory Region ◽  
Systematic Search ◽  
P Element ◽  
Regulatory Sequence ◽  
Cis Acting ◽  
The Third

P element transposition in Drosophila melanogaster is limited to the germ line because the third intron (the ORF2-ORF3 intron) of the P element transcript is spliced only in germ line cells. We describe a systematic search for P element sequences that are required to regulate the splicing of the ORF2-ORF3 intron. We have identified three adjacent mutations that abolish the germ line specificity and allow splicing of this intron in all tissues. These mutations define a 20-base regulatory region located in the exon, 12 to 31 bases from the 5' splice site. Our data show that this cis-acting regulatory sequence is required to inhibit the splicing of the ORF2-ORF3 intron in somatic cells.

scholarly journals The bldB Gene Encodes a Small Protein Required for Morphogenesis, Antibiotic Production, and Catabolite Control inStreptomyces coelicolor

1998 ◽  
Vol 180 (6) ◽  
pp. 1556-1562 ◽  
Author(s):  
Margaret K. Pope ◽  
Brian Green ◽  
Janet Westpheling
Keyword(s):  
Antibiotic Production ◽  
Regulatory Region ◽  
Morphological Development ◽  
Coding Region ◽  
Carbon Utilization ◽  
Reading Frame ◽  
Extracellular Signals ◽  
Promoter Fusion ◽  
Catabolite Control

ABSTRACT Mutants blocked at the earliest stage of morphological development in Streptomyces species are called bld mutants. These mutants are pleiotropically defective in the initiation of development, the ability to produce antibiotics, the ability to regulate carbon utilization, and the ability to send and/or respond to extracellular signals. Here we report the identification and partial characterization of a 99-amino-acid open reading frame (ORF99) that is capable of restoring morphogenesis, antibiotic production, and catabolite control to all of the bldB mutants. Of the existing bld mutants, bldB is of special interest because the phenotype of this mutant is the most pleiotropic. DNA sequence analysis of ORF99 from each of the existingbldB mutants identified base changes either within the coding region of the predicted protein or in the regulatory region of the gene. Primer extension analysis identified an apparent transcription start site. A promoter fusion to the xylEreporter gene showed that expression of bldB is apparently temporally regulated and that the bldB gene product is involved in the regulation of its own expression.

scholarly journals Identification of a calicivirus isolate of unknown origin

2003 ◽  
Vol 84 (10) ◽  
pp. 2837-2845 ◽  
Author(s):  
Angelika Oehmig ◽  
Mathias Büttner ◽  
Frank Weiland ◽  
William Werz ◽  
Klaus Bergemann ◽  
...  
Keyword(s):  
Cho Cells ◽  
Chinese Hamster ◽  
Unknown Origin ◽  
Open Reading Frames ◽  
Coding Region ◽  
Electron Microscopic ◽  
Significant Similarity ◽  
Western Blots ◽  
Reading Frame ◽  
A Minor

Chinese hamster ovary (CHO) cells manifesting striking cytopathogenic changes in culture were investigated to determine the causative agent. Electron microscopic analyses revealed viral particles of about 40 nm in diameter, displaying typical calicivirus morphology. To date, this virus, designated isolate 2117, exclusively replicates in CHO cells, achieving only moderate titres. After cloning, the coding region of 7928 nucleotides, the 3′ non-coding region and the poly(A) tail were sequenced. The genome consists of three open reading frames (ORFs), with the first and second ORF having the same reading frame. The overall genomic organization as well as the nucleotide sequence of isolate 2117 is most similar to that of a recently described canine calicivirus, but also shows significant similarity to the sequences of mink calicivirus and other caliciviruses within the genus Vesivirus. In Western blots, using antibodies against the viral protease, a stable, unprocessed 3CD protein of 68 kDa was identified in homogenates of 2117-infected CHO cells. Furthermore, antibodies raised against ORF 3 reacted with the respective protein in 2117-virions, demonstrating that this predicted 9 kDa protein is a minor structural component of the virion. In addition, an RT-PCR assay was established to detect 2117 viral RNA in biological products such as foetal bovine serum, which will aid the discovery of the origin and host of the virus.

scholarly journals Identification of a cis-acting sequence required for germ line-specific splicing of the P element ORF2-ORF3 intron.

1991 ◽  
Vol 11 (3) ◽  
pp. 1538-1546 ◽  
Author(s):  
A C Chain ◽  
S Zollman ◽  
J C Tseng ◽  
F A Laski
Keyword(s):  
Drosophila Melanogaster ◽  
Splice Site ◽  
Germ Line ◽  
Somatic Cells ◽  
Regulatory Region ◽  
Systematic Search ◽  
P Element ◽  
Regulatory Sequence ◽  
Cis Acting ◽  
The Third

P element transposition in Drosophila melanogaster is limited to the germ line because the third intron (the ORF2-ORF3 intron) of the P element transcript is spliced only in germ line cells. We describe a systematic search for P element sequences that are required to regulate the splicing of the ORF2-ORF3 intron. We have identified three adjacent mutations that abolish the germ line specificity and allow splicing of this intron in all tissues. These mutations define a 20-base regulatory region located in the exon, 12 to 31 bases from the 5' splice site. Our data show that this cis-acting regulatory sequence is required to inhibit the splicing of the ORF2-ORF3 intron in somatic cells.

scholarly journals Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Fanni Borvető ◽  
Ignacio G Bravo ◽  
Anouk Willemsen
Keyword(s):  
Recombination Event ◽  
Regulatory Element ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Regulatory Region ◽  
Open Reading Frames ◽  
Host Switch ◽  
Regulatory Changes ◽  
Evolution Of Gene Regulation ◽  
Reading Frames

Abstract Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus–host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and recombination, also appear to play an important role in PV evolution. In this study, we have examined the genomic impact of a recombination event between distantly related PVs infecting Cetartiodactyla (even-toed ungulates and cetaceans). Our phylogenetic analyses suggest that one single recombination was responsible for the generation of extant ‘chimeric’ PV genomes infecting cetaceans. By correlating the phylogenetic relationships to the genomic content, we observed important differences between the recombinant and non-recombinant cetartiodactyle PV genomes. Notably, recombinant PVs contain a unique set of conserved motifs in the upstream regulatory region (URR). We interpret these regulatory changes as an adaptive response to drastic changes in the PV genome. In terms of codon usage preferences (CUPrefs), we did not detect any particular differences between orthologous open reading frames in recombinant and non-recombinant PVs. Instead, our results are in line with previous observations suggesting that CUPrefs in PVs are rather linked to gene expression patterns as well as to gene function. We show that the non-coding URR of PVs infecting cetaceans, the central regulatory element in these viruses, exhibits signs of adaptation following a recombination event. Our results suggest that also in PVs, the evolution of gene regulation can play an important role in speciation and adaptation to novel environments.

scholarly journals Evolutionary conservation of homeodomain-binding sites and other sequences upstream and within the major transcription unit of the Drosophila segmentation gene engrailed.

1989 ◽  
Vol 9 (10) ◽  
pp. 4304-4311 ◽  
Author(s):  
J A Kassis ◽  
C Desplan ◽  
D K Wright ◽  
P H O'Farrell
Keyword(s):  
Binding Sites ◽  
Regulatory Region ◽  
Divergence Time ◽  
Evolutionary Conservation ◽  
Transcription Unit ◽  
Regulatory Proteins ◽  
Coding Region ◽  
Cis Acting ◽  
Perfect Sequence ◽  
Development Proceeds

The engrailed (en) gene functions throughout Drosophila development and is expressed in a succession of intricate spatial patterns as development proceeds. Normal en function relies on an extremely large cis-acting regulatory region (70 kilobases). We are using evolutionary conservation to help identify en sequences important in regulating patterned expression. Sequence comparison of 2.6 kilobases upstream of the en coding region of D. melanogaster and D. virilis (estimated divergence time, 60 million years) showed that 30% of this DNA occurs in islands of near perfect sequence conservation. One of these conserved islands contains binding sites for homeodomain-containing proteins. It has been shown genetically that homeodomain-containing proteins regulate en expression. Our data suggested that this regulation may be direct. The remaining conserved islands may contain binding sites for other regulatory proteins.

Correct temperature induction and developmental regulation of a cloned heat shock gene transformed into the Drosophila germ line

1984 ◽  
Vol 4 (12) ◽  
pp. 2883-2889
Author(s):  
E P Hoffman ◽  
V G Corces
Keyword(s):  
Heat Shock ◽  
Germ Line ◽  
Developmental Regulation ◽  
Heat Shock Gene ◽  
Coding Region ◽  
Chromosomal Locus ◽  
Base Pairs ◽  
Protein Coding ◽  
Reading Frame ◽  
Altered Gene

We have constructed a size variant of the Drosophila hsp28 gene by deleting 207 base pairs of the protein coding region, beginning 33 base pairs downstream of the ATG protein initiation codon. After transformation of Drosophila melanogaster rosy (ry506) flies with this altered gene, using the P transposable element system, it was found that the transformed gene was regulated correctly both after temperature elevation and during the development of the flies. Levels of the variant mRNA were as high as those of the endogenous hsp28 during all patterns of expression, and the variant mRNA appeared in all cases to be processed correctly and to be as stable as the endogenous mRNA. Nevertheless, the chromosomal locus of the transformed gene did not puff after heat shock, suggesting that normal transcription of the gene does not require puffing of the locus. The deleted hsp28 gene retained the reading frame of the endogenous one, and a protein of the expected molecular weight of 18,500 was made after heat shock at levels comparable to those of the endogenous hsp28.

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