scholarly journals Insertion of transposon Tn7 into the Escherichia coli glmS transcriptional terminator

1986 ◽  
Vol 234 (1) ◽  
pp. 111-117 ◽  
Author(s):  
N J Gay ◽  
V L Tybulewicz ◽  
J E Walker
Keyword(s):  
Escherichia Coli ◽  
Transposable Elements ◽  
Protein Sequence ◽  
Open Reading Frame ◽  
Base Pairs ◽  
Transcriptional Terminator ◽  
Reading Frame ◽  
High Frequencies ◽  
Unique Site ◽  
Dyad Symmetry

The transposon Tn7 is unusual as it transposes at high frequencies from episomal elements to a unique site in the Escherichia coli chromosome. This unique site is within a region of dyad symmetry that we have demonstrated to be the transcriptional terminator of the glmS gene which encodes the glutamine amidotransferase, glucosamine synthetase. Transposition of Tn7 abolishes termination of glmS transcription at this site; the transcripts now extend into the left end of Tn7 and terminate at a new site, tm, 127 base pairs from the left end of Tn7. This region of the transposon contains a long open reading frame which encodes a protein sequence that is significantly related to the transposase proteins of the transposable elements IS1 and Tn3. A weak transcript has been identified that emanates from a promoter on the 5′ side of this reading frame. This promoter is over-run by glmS transcripts and so it appears that expression of the Tn7 transposase may be regulated by promoter occlusion.

scholarly journals One of the tightly clustered genes of the mouse surfeit locus is a highly expressed member of a multigene family whose other members are predominantly processed pseudogenes.

1988 ◽  
Vol 8 (9) ◽  
pp. 3898-3905 ◽  
Author(s):  
C Huxley ◽  
T Williams ◽  
M Fried
Keyword(s):  
Multigene Family ◽  
Open Reading Frame ◽  
The Other ◽  
Base Pairs ◽  
Regulation Of Expression ◽  
Reading Frame ◽  
Processed Pseudogenes ◽  
Dna Fragment ◽  
Basic Polypeptide

The mouse surfeit locus is unusual in that it contains a number of closely clustered genes (Surf-1, -2, and -4) that alternate in their direction of transcription (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988). The heterogeneous 5' ends of Surf-1 and Surf-2 are separated by 15 to 73 base pairs (bp), and the 3' ends of Surf-2 and Surf-4 overlap by 133 bp (T. Williams and M. Fried, Mol. Cell. Biol. 6:4558-4569, 1986; T. Williams and M. Fried, Nature (London) 322:275-279, 1986). A fourth gene in this locus, Surf-3, which is a member of a multigene family, has been identified. The poly(A) addition site of Surf-3 lies only 70 bp from the poly(A) addition site of Surf-1. Transcription of Surf-3 has been studied in the absence of the other members of its multigene family after transfection of a cloned genomic mouse DNA fragment, containing the Surf-3 gene, into heterologous monkey cells. Surf-3 specifies a highly expressed 1.0-kilobase mRNA that contains a long open reading frame of 266 amino acids, which would encode a highly basic polypeptide (23% Arg plus Lys). The other members of the Surf-3 multigene family are predominantly, if not entirely, intronless pseudogenes with the hallmarks of being generated by reverse transcription. The role of the very tight clustering on regulation of expression of the genes in the surfeit locus is discussed.

scholarly journals Regulation of the nfsA Gene in Escherichia coli by SoxS

2002 ◽  
Vol 184 (1) ◽  
pp. 51-58 ◽  
Author(s):  
E. Suzanne Paterson ◽  
Sherri E. Boucher ◽  
I. B. Lambert
Keyword(s):  
Escherichia Coli ◽  
Promoter Sequence ◽  
Open Reading Frame ◽  
Base Sequence ◽  
Start Site ◽  
Transcription Start ◽  
Band Shift ◽  
Reading Frame ◽  
Shift Analysis ◽  
Small Open Reading Frame

ABSTRACT In Escherichia coli, the response to oxidative stress due to elevated levels of superoxide is mediated, in part, by the soxRS regulon. One member of the soxRS regulon, nfsA, encodes the major oxygen-insensitive nitroreductase in Escherichia coli which catalyzes the reduction of nitroaromatic and nitroheterocyclic compounds by NADPH. In this study we investigate the regulation of nfsA in response to the superoxide generating compound paraquat. The transcription start site (TSS) of nfsA was located upstream of the ybjC gene, a small open reading frame of unknown function located directly upstream of nfsA, suggesting that these two genes form an operon. The activity of the promoter associated with this TSS was confirmed with lacZ fusions and was shown to be inducible by paraquat. Footprinting and band shift analysis showed that purified His-tagged SoxS protein binds to a 20-base sequence 10 bases upstream of the −35 promoter sequence in the forward orientation, suggesting that the ybjC-nfsA promoter is a class I SoxS-dependent promoter.

S elements: a family of Tc1-like transposons in the genome of Drosophila melanogaster.

Genetics ◽  
1995 ◽  
Vol 141 (4) ◽  
pp. 1425-1438 ◽  
Author(s):  
P J Merriman ◽  
C D Grimes ◽  
J Ambroziak ◽  
D A Hackett ◽  
P Skinner ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Amino Acid ◽  
Transposable Elements ◽  
Sibling Species ◽  
Inverted Repeat ◽  
Open Reading Frame ◽  
Drosophila Species ◽  
Insertion Mutation ◽  
Reading Frame ◽  
Diploid Genome

Abstract The S elements form a diverse family of long-inverted-repeat transposons within the genome of Drosophila melanogaster. These elements vary in size and sequence, the longest consisting of 1736 bp with 234-bp inverted terminal repeats. The longest open reading frame in an intact S element could encode a 345-amino acid polypeptide. This polypeptide is homologous to the transposases of the mariner-Tc1 superfamily of transposable elements. S elements are ubiquitous in D. melanogaster populations and also appear to be present in the genomes of two sibling species; however, they seem to be absent from 17 other Drosophila species that were examined. Within D. melanogaster strains, there are, on average, 37.4 cytologically detectable S elements per diploid genome. These elements are scattered throughout the chromosomes, but several sites in both the euchromatin and beta heterochromatin are consistently occupied. The discovery of an S-element-insertion mutation and a reversion of this mutation indicates that S elements are at least occasionally mobile in the D. melanogaster genome. These elements seem to insert at an AT dinucleotide within a short palindrome and apparently duplicate that dinucleotide upon insertion.

The extrachromosomal replication of Dictyostelium plasmid Ddp2 requires a cis-acting element and a plasmid-encoded trans-acting factor

1990 ◽  
Vol 10 (7) ◽  
pp. 3727-3736
Author(s):  
B Leiting ◽  
I J Lindner ◽  
A A Noegel
Keyword(s):  
Escherichia Coli ◽  
Copy Number ◽  
Wild Strain ◽  
Open Reading Frame ◽  
Mobility Shift ◽  
Reading Frame ◽  
Cis Acting ◽  
Transformation Vector ◽  
Cis And Trans ◽  
Electrophoretic Mobility Shift Assays

Dictyostelium discoideum plasmid Ddp2 from the wild strain WS380B is a 5.8-kilobase (kb) supercoiled circle with a copy number of 300 per haploid genome. We previously described the construction of an extrachromosomally replicating transformation vector pnDeI carrying 4.7 kb of Ddp2 sequences (B. Leiting, and A. Noegel, Plasmid 20:241-248, 1988). In order to reduce the sequences required for extrachromosomal maintenance in D. discoideum, we characterized Ddp2 by sequence analysis, by deletion experiments, by transcription mapping, by electrophoretic mobility shift assays, and by expression of its single open reading frame in Escherichia coli. Two elements were involved in replication of Ddp2: a cis-acting sequence located on a 592-base-pair (bp) fragment that consisted of 220 bp of essential and 372 bp of auxiliary sequences, and a 2.7-kb open reading frame which most likely encodes a trans-acting factor. The cis- and trans-acting elements did not overlap and were shown to act independently from the location of the sequences encoding the trans-acting factor.

scholarly journals Identification of the ubiD Gene on theEscherichia coli Chromosome

2000 ◽  
Vol 182 (21) ◽  
pp. 6243-6246 ◽  
Author(s):  
Haitao Zhang ◽  
George T. Javor
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Gene Product ◽  
Mutant Strain ◽  
Amino Acid Residue ◽  
Open Reading Frame ◽  
Reading Frame

ABSTRACT The open reading frame at 86.7 min on the Escherichia coli chromosome, “yigC,” complemented aubiD mutant strain, AN66, indicating that yigCis the ubiD gene. The gene product, a 497-amino-acid-residue protein, showed extensive homology to the UPF 00096 family of proteins in the Swiss-Prot database.

scholarly journals CTF4 (CHL15) mutants exhibit defective DNA metabolism in the yeast Saccharomyces cerevisiae.

1992 ◽  
Vol 12 (12) ◽  
pp. 5736-5747 ◽  
Author(s):  
N Kouprina ◽  
E Kroll ◽  
V Bannikov ◽  
V Bliskovsky ◽  
R Gizatullin ◽  
...  
Keyword(s):  
Cell Division ◽  
Protein Sequence ◽  
Function Analysis ◽  
Spontaneous Mutation ◽  
Terminal Region ◽  
Open Reading Frame ◽  
Nucleotide Sequence Analysis ◽  
Dna Metabolism ◽  
Reading Frame ◽  
Helix Loop Helix

We have analyzed the CTF4 (CHL15) gene, earlier identified in two screens for yeast mutants with increased rates of mitotic loss of chromosome III and artificial circular and linear chromosomes. Analysis of the segregation properties of circular minichromosomes and chromosome fragments indicated that sister chromatid loss (1:0 segregation) is the predominant mode of chromosome destabilization in ctf4 mutants, though nondisjunction events (2:0 segregation) also occur at an increased rate. Both inter- and intrachromosomal mitotic recombination levels are elevated in ctf4 mutants, whereas spontaneous mutation to canavanine resistance was not elevated. A genomic clone of CTF4 was isolated and used to map its physical and genetic positions on chromosome XVI. Nucleotide sequence analysis of CTF4 revealed a 2.8-kb open reading frame with a 105-kDa predicted protein sequence. The CTF4 DNA sequence is identical to that of POB1, characterized as a gene encoding a protein that associates in vitro with DNA polymerase alpha. At the N-terminal region of the protein sequence, zinc finger motifs which define potential DNA-binding domains were found. The C-terminal region of the predicted protein displayed similarity to sequences of regulatory proteins known as the helix-loop-helix proteins. Data on the effects of a frameshift mutation suggest that the helix-loop-helix domain is essential for CTF4 function. Analysis of sequences upstream of the CTF4 open reading frame revealed the presence of a hexamer element, ACGCGT, a sequence associated with many DNA metabolism genes in budding yeasts. Disruption of the coding sequence of CTF4 did not result in inviability, indicating that the CTF4 gene is nonessential for mitotic cell division. However, ctf4 mutants exhibit an accumulation of large budded cells with the nucleus in the neck. ctf4 rad52 double mutants grew very slowly and produced extremely high levels (50%) of inviable cell division products compared with either single mutant alone, which is consistent with a role for CTF4 in DNA metabolism.

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