scholarly journals Minimal and Contributing Sequence Determinants of thecis-Acting Locus of Transfer (clt) of Streptomycete Plasmid pIJ101 Occur within an Intrinsically Curved Plasmid Region

2000 ◽  
Vol 182 (23) ◽  
pp. 6834-6841 ◽  
Author(s):  
Matthew J. Ducote ◽  
Shubha Prakash ◽  
Gregg S. Pettis
Keyword(s):  
Transfer Function ◽  
Inverted Repeat ◽  
Regulatory Gene ◽  
Direct Repeat ◽  
Higher Order ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Repeat Sequences ◽  
Inherent Feature ◽  
Close Proximity

ABSTRACT Efficient interbacterial transfer of streptomycete plasmid pIJ101 requires the pIJ101 tra gene, as well as acis-acting plasmid function known as clt. Here we show that the minimal pIJ101 clt locus consists of a sequence no greater than 54 bp in size that includes essential inverted-repeat and direct-repeat sequences and is located in close proximity to the 3′ end of the korB regulatory gene. Evidence that sequences extending beyond the minimal locus and into thekorB open reading frame influence clt transfer function and demonstration that clt-korB sequences are intrinsically curved raise the possibility that higher-order structuring of DNA and protein within this plasmid region may be an inherent feature of efficient pIJ101 transfer.

scholarly journals The Cloning and Molecular Analysis of pawn-B in Paramecium tetraurelia

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1105-1117 ◽  
Author(s):  
W John Haynes ◽  
Kit-Yin Ling ◽  
Robin R Preston ◽  
Yoshiro Saimi ◽  
Ching Kung
Keyword(s):  
Genomic Library ◽  
Open Reading Frame ◽  
Paramecium Tetraurelia ◽  
Wild Type ◽  
Rt Pcr ◽  
Reading Frame ◽  
Close Proximity ◽  
In The Wild ◽  
Dna Fragment ◽  
Alternative Sites

Abstract Pawn mutants of Paramecium tetraurelia lack a depolarization-activated Ca2+ current and do not swim backward. Using the method of microinjection and sorting a genomic library, we have cloned a DNA fragment that complements pawn-B (pwB/pwB). The minimal complementing fragment is a 798-bp open reading frame (ORF) that restores the Ca2+ current and the backward swimming when expressed. This ORF contains a 29-bp intron and is transcribed and translated. The translated product has two putative transmembrane domains but no clear matches in current databases. Mutations in the available pwB alleles were found within this ORF. The d4-95 and d4-96 alleles are single base substitutions, while d4-662 (previously pawn-D) harbors a 44-bp insertion that matches an internal eliminated sequence (IES) found in the wild-type germline DNA except for a single C-to-T transition. Northern hybridizations and RT-PCR indicate that d4-662 transcripts are rapidly degraded or not produced. A second 155-bp IES in the wild-type germline ORF excises at two alternative sites spanning three asparagine codons. The pwB ORF appears to be separated from a 5′ neighboring ORF by only 36 bp. The close proximity of the two ORFs and the location of the pwB protein as indicated by GFP-fusion constructs are discussed.

scholarly journals GIT1, a Gene Encoding a Novel Transporter for Glycerophosphoinositol in Saccharomyces cerevisiae

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 1707-1715 ◽  
Author(s):  
J L Patton-Vogt ◽  
S A Henry
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Regulatory Gene ◽  
Sugar Transport ◽  
Open Reading Frame ◽  
Gene Encoding ◽  
Reading Frame ◽  
Membrane Spanning ◽  
Membrane Spanning Domains ◽  
Uptake And Metabolism ◽  
Cells Cultured

Abstract Phosphatidylinositol catabolism in Saccharomyces cerevisiae cells cultured in media containing inositol results in the release of glycerophosphoinositol (GroPIns) into the medium. As the extracellular concentration of inositol decreases with growth, the released GroPIns is transported back into the cell. Exploiting the ability of the inositol auxotroph, ino1, to use exogenous GroPIns as an inositol source, we have isolated mutants (Git−) defective in the uptake and metabolism of GroPIns. One mutant was found to be affected in the gene encoding the transcription factor, SPT7. Mutants of the positive regulatory gene INO2, but not of its partner, INO4, also have the Git− phenotype. Another mutant was complemented by a single open reading frame (ORF) termed GIT1 (glycerophosphoinositol). This ORF consists of 1556 bp predicted to encode a polypeptide of 518 amino acids and 57.3 kD. The predicted Git1p has similarity to a variety of S. cerevisiae transporters, including a phosphate transporter (Pho84p), and both inositol transporters (Itr1p and Itr2p). Furthermore, Git1p contains a sugar transport motif and 12 potential membrane-spanning domains. Transport assays performed on a git1 mutant together with the above evidence indicate that the GIT1 gene encodes a permease involved in the uptake of GroPIns.

The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1

1988 ◽  
Vol 8 (4) ◽  
pp. 1432-1442 ◽  
Author(s):  
J D Boeke ◽  
D Eichinger ◽  
D Castrillon ◽  
G R Fink
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Long Terminal Repeat ◽  
Missense Mutation ◽  
Dna Sequence ◽  
Open Reading Frame ◽  
Yeast Genome ◽  
Reading Frame ◽  
Ty Elements ◽  
Ty Element ◽  
Repeat Sequences

Saccharomyces cerevisiae Ty elements are transposons closely related to retroviruses. The DNA sequence of a functional Ty element (TyH3) is presented. The long terminal repeat sequences are different, suggesting that TyH3 is a recombinant Ty element. A chromosomal Ty element near the LYS2 gene, Ty173, was found to be nonfunctional, even though it has no detectable insertions or deletions. The defect in Ty173 transposition is caused by a missense mutation giving rise to a Leu-to-Ile substitution in the TYB (pol) open reading frame. Several chromosomal Ty elements carry this lesion in their DNA, indicating that nonfunctional Ty elements are common in the yeast genome.

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.

scholarly journals Comparative Biology of Two Natural Variants of the IncQ-2 Family Plasmids, pRAS3.1 and pRAS3.2

2009 ◽  
Vol 191 (20) ◽  
pp. 6436-6446 ◽  
Author(s):  
Wesley Loftie-Eaton ◽  
Douglas E. Rawlings
Keyword(s):  
Copy Number ◽  
Promoter Region ◽  
Plasmid Stability ◽  
Inducible Promoter ◽  
Open Reading Frame ◽  
Comparative Biology ◽  
Incompatibility Group ◽  
Reading Frame ◽  
Repeat Sequences ◽  
Natural Variants

ABSTRACT Plasmids pRAS3.1 and pRAS3.2 are two closely related, natural variants of the IncQ-2 plasmid family that have identical plasmid backbones except for two differences. Plasmid pRAS3.1 has five 6-bp repeat sequences in the promoter region of the mobB gene and four 22-bp iterons in its oriV region, whereas pRAS3.2 has only four 6-bp repeats and three 22-bp iterons. Plasmid pRAS3.1 was found to have a higher copy number than pRAS3.2, and we show that the extra 6-bp repeat results in an increase in mobB and downstream mobA/repB expression. Placement of repB (primase) behind an arabinose-inducible promoter in trans resulted in an increase in repB expression and an approximately twofold increase in the copy number of plasmids with identical numbers of 22-bp iterons. The pRAS3 plasmids were shown to have a previously unrecognized toxin-antitoxin plasmid stability module within their replicons. The ability of the pRAS3 plasmids to mobilize the oriT regions of two other plasmids of the IncQ-2 family, pTF-FC2 and pTC-F14, suggested that the mobilization proteins pRAS3 are relaxed and can mobilize oriT regions with substantially different sequences. Plasmids pRAS3.1 and pRAS3.2 were highly incompatible with plasmids pTF-FC2 and pTC-F14, and this incompatibility was removed on inactivation of an open reading frame situated downstream of the mobCDE mobilization genes rather than being due to the 22-bp oriV-associated iterons. We propose that the pRAS3 plasmids represent a third, γ incompatibility group within the IncQ-2 family plasmids.

scholarly journals The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1.

1988 ◽  
Vol 8 (4) ◽  
pp. 1432-1442 ◽  
Author(s):  
J D Boeke ◽  
D Eichinger ◽  
D Castrillon ◽  
G R Fink
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Long Terminal Repeat ◽  
Missense Mutation ◽  
Dna Sequence ◽  
Open Reading Frame ◽  
Yeast Genome ◽  
Reading Frame ◽  
Ty Elements ◽  
Ty Element ◽  
Repeat Sequences

Saccharomyces cerevisiae Ty elements are transposons closely related to retroviruses. The DNA sequence of a functional Ty element (TyH3) is presented. The long terminal repeat sequences are different, suggesting that TyH3 is a recombinant Ty element. A chromosomal Ty element near the LYS2 gene, Ty173, was found to be nonfunctional, even though it has no detectable insertions or deletions. The defect in Ty173 transposition is caused by a missense mutation giving rise to a Leu-to-Ile substitution in the TYB (pol) open reading frame. Several chromosomal Ty elements carry this lesion in their DNA, indicating that nonfunctional Ty elements are common in the yeast genome.

scholarly journals Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5' leader.

1987 ◽  
Vol 7 (8) ◽  
pp. 2728-2734 ◽  
Author(s):  
C A Strick ◽  
T D Fox
Keyword(s):  
Amino Acids ◽  
Regulatory Gene ◽  
Mitochondrial Protein ◽  
Nuclear Gene ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Amino Terminal ◽  
Interesting Pattern ◽  
Reading Frames

The yeast nuclear gene PET111 is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET111. The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PET111 gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PET111 fused to beta-galactosidase is specifically associated with mitochondria. PET111 is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET111 reading frame.

scholarly journals DNA sequence homology between the terminal inverted repeats of Shope fibroma virus and an endogenous cellular plasmid species

1986 ◽  
Vol 6 (1) ◽  
pp. 265-276
Author(s):  
C Upton ◽  
G McFadden
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sequence Homology ◽  
Inverted Repeat ◽  
Specific Activity ◽  
High Specific Activity ◽  
Cesium Chloride ◽  
Open Reading Frame ◽  
Terminal Inverted Repeat ◽  
Reading Frame

DNA hybridization experiments indicate that the genome of a tumorigenic poxvirus. Shope fibroma virus (SFV), possesses sequence homology with DNA isolated from uninfected rabbit cells. Southern blotting experiments, either with high-complexity rabbit DNA as probe and SFV restriction fragments as targets or with high-specific activity, 32P-labeled, cloned SFV sequences as probes and rabbit DNA as target, indicate that the homologous sequences map at two locations within the viral genome, one in each copy of the terminal inverted repeat sequences. Unexpectedly, Southern blots revealed that the homologous host sequences reside in a rabbit extrachromosomal DNA element. This autonomous low-molecular-weight DNA species could be specifically amplified by cycloheximide treatment and was shown by isopycnic centrifugation in cesium chloride-ethidium bromide to consist predominantly of covalently closed circular DNA molecules. DNA sequencing of pSIC-9, a cloned 1.9-kilobase fragment of the rabbit plasmid species, indicated extensive homology at the nucleotide level over a 1.5-kilobase stretch of the viral terminal inverted repeat. Analysis of open reading frames in both the plasmid and SFV DNA revealed that (i) the N-terminal 157-amino acid sequence of a potential 514-amino acid SFV polypeptide is identical to the N-terminal 157 amino acids of one pSIC-9 open reading frame, and (ii) a second long pSIC-9 open reading frame of 361 amino acids, although significantly diverged from the comparable nucleotide sequence in the virus, possessed considerable homology to a family of cellular protease inhibitors, including alpha 1-antichymotrypsin, alpha 1-antitrypsin, and antithrombin III. The potential role of such cellular plasmid-like DNA species as a mediator in the exchange of genetic information between the host cell and a cytoplasmically replicating poxvirus is discussed.

scholarly journals A Streptomyces coelicolor Antibiotic Regulatory Gene, absB, Encodes an RNase III Homolog

1999 ◽  
Vol 181 (19) ◽  
pp. 6142-6151 ◽  
Author(s):  
Brenda Price ◽  
Trifon Adamidis ◽  
Renqui Kong ◽  
Wendy Champness
Keyword(s):  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Regulatory Gene ◽  
Open Reading Frame ◽  
Dependent Manner ◽  
Rnase Iii ◽  
Reading Frame ◽  
E Coli ◽  
Lines Of Evidence ◽  
Global Defect

ABSTRACT Streptomyces coelicolor produces four genetically and structurally distinct antibiotics in a growth-phase-dependent manner.S. coelicolor mutants globally deficient in antibiotic production (Abs− phenotype) have previously been isolated, and some of these were found to define the absB locus. In this study, we isolated absB-complementing DNA and show that it encodes the S. coelicolor homolog of RNase III (rnc). Several lines of evidence indicate that theabsB mutant global defect in antibiotic synthesis is due to a deficiency in RNase III. In marker exchange experiments, the S. coelicolor rnc gene rescued absB mutants, restoring antibiotic production. Sequencing the DNA of absB mutants confirmed that the absB mutations lay in thernc open reading frame. Constructed disruptions ofrnc in both S. coelicolor 1501 andStreptomyces lividans 1326 caused an Abs−phenotype. An absB mutation caused accumulation of 30S rRNA precursors, as had previously been reported for E. coli rncmutants. The absB gene is widely conserved in streptomycetes. We speculate on why an RNase III deficiency could globally affect the synthesis of antibiotics.

Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5' leader

1987 ◽  
Vol 7 (8) ◽  
pp. 2728-2734
Author(s):  
C A Strick ◽  
T D Fox
Keyword(s):  
Amino Acids ◽  
Regulatory Gene ◽  
Mitochondrial Protein ◽  
Nuclear Gene ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Amino Terminal ◽  
Interesting Pattern ◽  
Reading Frames

The yeast nuclear gene PET111 is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET111. The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PET111 gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PET111 fused to beta-galactosidase is specifically associated with mitochondria. PET111 is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET111 reading frame.

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