Yeast regulatory gene GAL3: carbon regulation; UASGal elements in common with GAL1, GAL2, GAL7, GAL10, GAL80, and MEL1; encoded protein strikingly similar to yeast and Escherichia coli galactokinases

1988 ◽  
Vol 8 (8) ◽  
pp. 3439-3447 ◽  
Author(s):  
W Bajwa ◽  
T E Torchia ◽  
J E Hopper
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Regulatory Gene ◽  
Data Bank ◽  
Noncoding Region ◽  
Striking Similarity ◽  
Coding Region ◽  
Reading Frame ◽  
Carbon Regulation ◽  
Sequence Similarities

GAL3 gene expression is required for rapid GAL4-mediated galactose induction of the galactose-melibiose regulon genes in Saccharomyces cerevisiae. Here we show by Northern (RNA) blot analysis that GAL3 gene expression is itself galactose inducible. Like the GAL1, GAL7, GAL10, and MEL1 genes, the GAL3 gene is severely glucose repressed. Like the MEL1 gene, but in contrast to the GAL1, GAL7, and GAL10 genes, GAL3 is expressed at readily detectable basal levels in cells grown in noninducing, nonrepressing media. We determined the sequence of the S. cerevisiae GAL3 gene and its 5'-noncoding region. Within the 5'-noncoding region of the GAL3 gene, we found two sequences similar to the UASGal elements of the other galactose-melibiose regulon genes. Deletion analysis indicated that only the most ATG proximal of these sequences is required for GAL3 expression. The coding region of GAL3 consists of a 1,275-base-pair open reading frame in the direction of transcription. A comparison of the deduced 425-amino-acid sequence with the protein data bank revealed three regions of striking similarity between the GAL3 protein and the GAL1-specified galactokinase of Saccharomyces carlsbergensis. One of these regions also showed striking similarity to sequences within the galactokinase protein of Escherichia coli. On the basis of these protein sequence similarities, we propose that the GAL3 protein binds a molecule identical to or structurally related to one of the substrates or products of the galactokinase-catalyzed reaction.

scholarly journals Yeast regulatory gene GAL3: carbon regulation; UASGal elements in common with GAL1, GAL2, GAL7, GAL10, GAL80, and MEL1; encoded protein strikingly similar to yeast and Escherichia coli galactokinases.

1988 ◽  
Vol 8 (8) ◽  
pp. 3439-3447 ◽  
Author(s):  
W Bajwa ◽  
T E Torchia ◽  
J E Hopper
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Regulatory Gene ◽  
Data Bank ◽  
Noncoding Region ◽  
Striking Similarity ◽  
Coding Region ◽  
Reading Frame ◽  
Carbon Regulation ◽  
Sequence Similarities

GAL3 gene expression is required for rapid GAL4-mediated galactose induction of the galactose-melibiose regulon genes in Saccharomyces cerevisiae. Here we show by Northern (RNA) blot analysis that GAL3 gene expression is itself galactose inducible. Like the GAL1, GAL7, GAL10, and MEL1 genes, the GAL3 gene is severely glucose repressed. Like the MEL1 gene, but in contrast to the GAL1, GAL7, and GAL10 genes, GAL3 is expressed at readily detectable basal levels in cells grown in noninducing, nonrepressing media. We determined the sequence of the S. cerevisiae GAL3 gene and its 5'-noncoding region. Within the 5'-noncoding region of the GAL3 gene, we found two sequences similar to the UASGal elements of the other galactose-melibiose regulon genes. Deletion analysis indicated that only the most ATG proximal of these sequences is required for GAL3 expression. The coding region of GAL3 consists of a 1,275-base-pair open reading frame in the direction of transcription. A comparison of the deduced 425-amino-acid sequence with the protein data bank revealed three regions of striking similarity between the GAL3 protein and the GAL1-specified galactokinase of Saccharomyces carlsbergensis. One of these regions also showed striking similarity to sequences within the galactokinase protein of Escherichia coli. On the basis of these protein sequence similarities, we propose that the GAL3 protein binds a molecule identical to or structurally related to one of the substrates or products of the galactokinase-catalyzed reaction.

scholarly journals Physiological Studies of Escherichia coli Strain MG1655: Growth Defects and Apparent Cross-Regulation of Gene Expression

2003 ◽  
Vol 185 (18) ◽  
pp. 5611-5626 ◽  
Author(s):  
Eric Soupene ◽  
Wally C. van Heeswijk ◽  
Jacqueline Plumbridge ◽  
Valley Stewart ◽  
Daniel Bertenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Dna Microarrays ◽  
Degradation Products ◽  
Regulatory Gene ◽  
Regulation Of Gene Expression ◽  
Nitrate Respiration ◽  
Starch Degradation ◽  
Strain Mg1655 ◽  
Growth Defects

ABSTRACT Escherichia coli strain MG1655 was chosen for sequencing because the few mutations it carries (ilvG rfb-50 rph-1) were considered innocuous. However, it has a number of growth defects. Internal pyrimidine starvation due to polarity of the rph-1 allele on pyrE was problematic in continuous culture. Moreover, the isolate of MG1655 obtained from the E. coli Genetic Stock Center also carries a large deletion around the fnr (fumarate-nitrate respiration) regulatory gene. Although studies on DNA microarrays revealed apparent cross-regulation of gene expression between galactose and lactose metabolism in the Stock Center isolate of MG1655, this was due to the occurrence of mutations that increased lacY expression and suppressed slow growth on galactose. The explanation for apparent cross-regulation between galactose and N-acetylglucosamine metabolism was similar. By contrast, cross-regulation between lactose and maltose metabolism appeared to be due to generation of internal maltosaccharides in lactose-grown cells and may be physiologically significant. Lactose is of restricted distribution: it is normally found together with maltosaccharides, which are starch degradation products, in the mammalian intestine. Strains designated MG1655 and obtained from other sources differed from the Stock Center isolate and each other in several respects. We confirmed that use of other E. coli strains with MG1655-based DNA microarrays works well, and hence these arrays can be used to study any strain of interest. The responses to nitrogen limitation of two urinary tract isolates and an intestinal commensal strain isolated recently from humans were remarkably similar to those of MG1655.

scholarly journals Alternate RNA splicing of murine nfkb1 generates a nuclear isoform of the p50 precursor NF-kappa B1 that can function as a transactivator of NF-kappa B-regulated transcription.

1994 ◽  
Vol 14 (12) ◽  
pp. 8460-8470 ◽  
Author(s):  
R J Grumont ◽  
J Fecondo ◽  
S Gerondakis
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Rna Splicing ◽  
Coding Region ◽  
Nf Kappa B ◽  
Reading Frame ◽  
C Terminus ◽  
A Cell ◽  
Regulated Gene Expression

The NF-kappa B1 subunit of the transcription factor NF-kappa B is derived by proteolytic cleavage from the N terminus of a 105-kDa precursor protein. The C terminus of p105NF-kappa B1, like those of I kappa B proteins, contains ankyrin-related repeats that inhibit DNA binding and nuclear localization of the precursor and confer I kappa B-like properties upon p105NF-kappa B1. Here we report the characterization of two novel NF-kappa B1 precursor isoforms, p84NF-kappa B1 and p98NF-kappa B1, that arise by alternate splicing within the C-terminal coding region of murine nfkb1. p98NF-kappa B1, which lacks the 111 C-terminal amino acids (aa) of p105NF-kappa B1, has a novel 35-aa C terminus encoded by an alternate reading frame of the gene. p84NF-kappa B1 lacks the C-terminal 190 aa of p105NF-kappa B1, including part of ankyrin repeat 7. RNA and protein analyses indicated that the expression of p84NF-kappa B1 and p98NF-kappa B1 is restricted to certain tissues and that the phorbol myristate acetate-mediated induction of p84NF-kappa B1 and p105NF-kappa B1 differs in a cell-type-specific manner. Both p84NF-kappa B1 and p98NF-kappa B1 are found in the nuclei of transfected cells. Transient transfection analysis revealed that p98NF-kappa B1, but not p105NF-kappa B1 or p84NF-kappa B1, acts as a transactivator of NF-kappa B-regulated gene expression and that this is dependent on sequences in the Rel homology domain required for DNA binding and on the novel 35 C-terminal aa of this isoform. In contrast to previous findings, which indicated that p105NF-kappa B1 does not bind DNA, all of the NF-kappa B1 precursors were found to specifically bind with low affinity to a highly restricted set of NF-kappa B sites in vitro, thereby raising the possibility that certain of the NF-kappa B1 precursor isoforms may directly modulate gene expression.

Cloning and characterization of theddsAgene encoding decaprenyl diphosphate synthase fromRhodobacter capsulatusB10

2006 ◽  
Vol 52 (12) ◽  
pp. 1141-1147 ◽  
Author(s):  
Xinyi Liu ◽  
Haizhen Wu ◽  
Jiang Ye ◽  
Qinsheng Yuan ◽  
Huizhan Zhang
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Rhodobacter Capsulatus ◽  
Open Reading Frame ◽  
High Similarity ◽  
Reading Frame ◽  
Endogenous Production ◽  
Genome Library

A decaprenyl diphosphate synthase gene (ddsA, GenBank accession No. DQ191802) was cloned from Rhodobacter capsulatus B10 by constructing and screening the genome library. An open reading frame of 1002 bp was revealed from sequence analysis. The deduced polypeptide consisted of 333 amino acids residues with an molecular mass of about 37 kDa. The DdsA protein contained the conserved amino acid sequence (DDXXD) of E-type polyprenyl diphosphate synthase and showed high similarity to others. In contrast, DdsA showed only 39% identity to a solanesyl diphosphate synthase cloned from R. capsulatus SB1003. DdsA was expressed successfully in Escherichia coli. Assaying the enzyme in vivo found it made E.coli synthesize UQ-10 in addition to the endogenous production UQ-8.Key words: ubiquinone, polyprenyl diphosphate synthase, gene expression, Rhodobacter capsulatus.

scholarly journals YojI of Escherichia coli Functions as a Microcin J25 Efflux Pump

2005 ◽  
Vol 187 (10) ◽  
pp. 3465-3470 ◽  
Author(s):  
Mónica A. Delgado ◽  
Paula A. Vincent ◽  
Ricardo N. Farías ◽  
Raúl A. Salomón
Keyword(s):  
Escherichia Coli ◽  
Efflux Pump ◽  
Open Reading Frame ◽  
Peptide Antibiotic ◽  
Toxic Level ◽  
Reading Frame ◽  
Increased Sensitivity ◽  
Multicopy Vector ◽  
Microcin J25 ◽  
Sequence Similarities

ABSTRACT In the present study, we showed that yojI, an Escherichia coli open reading frame with an unknown function, mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. Disruption of the single chromosomal copy of yojI increased sensitivity of cells to microcin J25. The YojI protein was previously assumed to be an ATP-binding-cassette-type exporter on the basis of sequence similarities. We demonstrate that YojI is capable of pumping out microcin molecules. Thus, one obvious explanation for the protective effect against microcin J25 is that YojI action keeps the intracellular concentration of the peptide below a toxic level. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.

Salt-Induced Stability of SR1/CAMTA3 mRNA Is Mediated by Reactive Oxygen Species and Requires the 3’ End of Its Open Reading Frame

2020 ◽  
Vol 61 (4) ◽  
pp. 748-760
Author(s):  
Amira A E Abdel-Hameed ◽  
Kasavajhala V S K Prasad ◽  
Qiyan Jiang ◽  
Anireddy S N Reddy
Keyword(s):  
Gene Expression ◽  
Reactive Oxygen Species ◽  
Salt Stress ◽  
Crop Yields ◽  
Reactive Oxygen ◽  
Oxygen Species ◽  
Coding Region ◽  
Nonsense Mediated Decay ◽  
Reading Frame ◽  
Transcript Stability

Abstract Soil salinity, a prevalent abiotic stress, causes enormous losses in global crop yields annually. Previous studies have shown that salt stress-induced reprogramming of gene expression contributes to the survival of plants under this stress. However, mechanisms regulating gene expression in response to salt stress at the posttranscriptional level are not well understood. In this study, we show that salt stress increases the level of Signal Responsive 1 (SR1) mRNA, a member of signal-responsive Ca2+/calmodulin-regulated transcription factors, by enhancing its stability. We present multiple lines of evidence indicating that reactive oxygen species generated by NADPH oxidase activity mediate salt-induced SR1 transcript stability. Using mutants impaired in either nonsense-mediated decay, XRN4 or mRNA decapping pathways, we show that neither the nonsense-mediated mRNA decay pathway, XRN4 nor the decapping of SR1 mRNA is required for its decay. We analyzed the salt-induced accumulation of eight truncated versions of the SR1 coding region (∼3 kb) in the sr1 mutant background. This analysis identified a 500-nt region at the 3’ end of the SR1 coding region to be required for the salt-induced stability of SR1 mRNA. Potential mechanisms by which this region confers SR1 transcript stability in response to salt are discussed.

scholarly journals qnrD, a Novel Gene Conferring Transferable Quinolone Resistance in Salmonella enterica Serovar Kentucky and Bovismorbificans Strains of Human Origin

2008 ◽  
Vol 53 (2) ◽  
pp. 603-608 ◽  
Author(s):  
L. M. Cavaco ◽  
H. Hasman ◽  
S. Xia ◽  
F. M. Aarestrup
Keyword(s):  
Escherichia Coli ◽  
Plasmid Dna ◽  
Brain Heart Infusion ◽  
Open Reading Frame ◽  
Human Origin ◽  
Coding Region ◽  
Reading Frame ◽  
Brain Heart Infusion Agar ◽  
Vector Pbr322 ◽  
Infusion Agar

ABSTRACT In a previous study, four Salmonella isolates from humans in the Henan province of China showed reduced susceptibility to ciprofloxacin (MIC, 0.125 to 0.25 μg/ml) but were susceptible to nalidixic acid (MIC, 4 to 8 μg/ml). All isolates were negative for known qnr genes (A, B, and S), aac(6′)Ib-cr, and mutations in gyrA and parC. Plasmid DNA was extracted from all four isolates and transformed into Escherichia coli TG1 and DH10B cells by electroporation, and transformants were selected on 0.06 μg/ml ciprofloxacin containing brain heart infusion agar plates. Resistance to ciprofloxacin could be transferred by electroporation, and a similar 4,270-bp plasmid was found in all transformants. By sequence analysis, the plasmid was found to carry an open reading frame that had similarities to other qnr genes and that encoded a 214-amino-acid pentapeptide repeat protein. This gene, designated qnrD, showed 48% similarity to qnrA1, 61% similarity to qnrB1, and 41% similarity to qnrS1. Further subcloning of the qnrD coding region into the constitutively expressed tetA gene of vector pBR322 showed that the gene conferred an increase in the MIC of ciprofloxacin by a factor of 32 (from an MIC of 0.002 to an MIC of 0.06 μg/ml). For comparison, qnrA1 and qnrS1 were also subcloned into pBR322 and transformed into DH10B cells, conferring MICs of 0.125 and 0.5 μg/ml, respectively. A phylogenetic analysis of all known qnr sequences was performed and showed that qnrD was more closely related to the qnrB variants but formed an independent cluster. To our knowledge, this is the first description of this qnrD gene.

Alternate RNA splicing of murine nfkb1 generates a nuclear isoform of the p50 precursor NF-kappa B1 that can function as a transactivator of NF-kappa B-regulated transcription

1994 ◽  
Vol 14 (12) ◽  
pp. 8460-8470
Author(s):  
R J Grumont ◽  
J Fecondo ◽  
S Gerondakis
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Rna Splicing ◽  
Coding Region ◽  
Nf Kappa B ◽  
Reading Frame ◽  
C Terminus ◽  
A Cell ◽  
Regulated Gene Expression

The NF-kappa B1 subunit of the transcription factor NF-kappa B is derived by proteolytic cleavage from the N terminus of a 105-kDa precursor protein. The C terminus of p105NF-kappa B1, like those of I kappa B proteins, contains ankyrin-related repeats that inhibit DNA binding and nuclear localization of the precursor and confer I kappa B-like properties upon p105NF-kappa B1. Here we report the characterization of two novel NF-kappa B1 precursor isoforms, p84NF-kappa B1 and p98NF-kappa B1, that arise by alternate splicing within the C-terminal coding region of murine nfkb1. p98NF-kappa B1, which lacks the 111 C-terminal amino acids (aa) of p105NF-kappa B1, has a novel 35-aa C terminus encoded by an alternate reading frame of the gene. p84NF-kappa B1 lacks the C-terminal 190 aa of p105NF-kappa B1, including part of ankyrin repeat 7. RNA and protein analyses indicated that the expression of p84NF-kappa B1 and p98NF-kappa B1 is restricted to certain tissues and that the phorbol myristate acetate-mediated induction of p84NF-kappa B1 and p105NF-kappa B1 differs in a cell-type-specific manner. Both p84NF-kappa B1 and p98NF-kappa B1 are found in the nuclei of transfected cells. Transient transfection analysis revealed that p98NF-kappa B1, but not p105NF-kappa B1 or p84NF-kappa B1, acts as a transactivator of NF-kappa B-regulated gene expression and that this is dependent on sequences in the Rel homology domain required for DNA binding and on the novel 35 C-terminal aa of this isoform. In contrast to previous findings, which indicated that p105NF-kappa B1 does not bind DNA, all of the NF-kappa B1 precursors were found to specifically bind with low affinity to a highly restricted set of NF-kappa B sites in vitro, thereby raising the possibility that certain of the NF-kappa B1 precursor isoforms may directly modulate gene expression.

scholarly journals S-Methylmethionine Metabolism in Escherichia coli

1999 ◽  
Vol 181 (2) ◽  
pp. 662-665 ◽  
Author(s):  
Martin Thanbichler ◽  
Bernhard Neuhierl ◽  
August Böck
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Sequence Similarity ◽  
Physiological Role ◽  
High Sequence Similarity ◽  
Reading Frame ◽  
Amino Acid Permeases ◽  
Sequence Similarities ◽  
Homocysteine Methyltransferase

ABSTRACT Selenium-accumulating Astragalus spp. contain an enzyme which specifically transfers a methyl group fromS-methylmethionine to the selenol of selenocysteine, thus converting it to a nontoxic, since nonproteinogenic, amino acid. Analysis of the amino acid sequence of this enzyme revealed thatEscherichia coli possesses a protein (YagD) which shares high sequence similarity with the enzyme. The properties and physiological role of YagD were investigated. YagD is anS-methylmethionine: homocysteine methyltransferase which also accepts selenohomocysteine as a substrate. Mutants inyagD which also possess defects in metE andmetH are unable to utilize S-methylmethionine for growth, whereas a metE metH double mutant still grows on S-methylmethionine. Upstream of yagD and overlapping with its reading frame is a gene (ykfD) which, when inactivated, also blocks growth on methylmethionine in ametE metH genetic background. Since it displays sequence similarities with amino acid permeases it appears to be the transporter for S-methylmethionine. Methionine but notS-methylmethionine in the medium reduces the amount ofyagD protein. This and the existence of four MET box motifs upstream of yfkD indicate that the two genes are members of the methionine regulon. The physiological roles of the ykfDand yagD products appear to reside in the acquisition ofS-methylmethionine, which is an abundant plant product, and its utilization for methionine biosynthesis.

scholarly journals Identification and Mapping of Self-Assembling Protein Domains Encoded by the Escherichia coli K-12 Genome by Use of λ Repressor Fusions

2004 ◽  
Vol 186 (5) ◽  
pp. 1311-1319 ◽  
Author(s):  
Leonardo Mariño-Ramírez ◽  
Jonathan L. Minor ◽  
Nicola Reading ◽  
James C. Hu
Keyword(s):  
Escherichia Coli ◽  
Genomic Sequence ◽  
Data Bank ◽  
Coiled Coils ◽  
Reading Frame ◽  
Protein Fragments ◽  
E Coli ◽  
Self Assembling ◽  
K 12 ◽  
Novel Structures

ABSTRACT Self-assembling proteins and protein fragments encoded by the Escherichia coli genome were identified from E. coli K-12 strain MG1655. Libraries of random DNA fragments cloned into a series of λ repressor fusion vectors were subjected to selection for immunity to infection by phage λ. Survivors were identified by sequencing the ends of the inserts, and the fused protein sequence was inferred from the known genomic sequence. Four hundred sixty-three nonredundant open reading frame-encoded interacting sequence tags (ISTs) were recovered from sequencing 2,089 candidates. These ISTs, which range from 16 to 794 amino acids in length, were clustered into families of overlapping fragments, identifying potential homotypic interactions encoded by 232 E. coli genes. Repressor fusions identified ISTs from genes in every protein-based functional category, but membrane proteins were underrepresented. The IST-containing genes were enriched for regulatory proteins and for proteins that form higher-order oligomers. Forty-eight (20.7%) homotypic proteins identified by ISTs are predicted to contain coiled coils. Although most of the IST-containing genes are identifiably related to proteins in other bacterial genomes, more than half of the ISTs do not have identifiable homologs in the Protein Data Bank, suggesting that they may include many novel structures. The data are available online at http://oligomers.tamu.edu/ .

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