scholarly journals Structural and Functional Analysis of the Phosphonoacetate Hydrolase (phnA) Gene Region in Pseudomonas fluorescens 23F

2001 ◽  
Vol 183 (11) ◽  
pp. 3268-3275 ◽  
Author(s):  
Anna N. Kulakova ◽  
Leonid A. Kulakov ◽  
Natalya V. Akulenko ◽  
Vladimir N. Ksenzenko ◽  
John T. G. Hamilton ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Bond Cleavage ◽  
Transcriptional Regulators ◽  
Open Reading Frames ◽  
Cell Analysis ◽  
Rna Analysis ◽  
Cleavage Enzyme ◽  
Reading Frames ◽  
Lysr Family ◽  
In Cells

ABSTRACT The Pseudomonas fluorescens 23F phosphonoacetate hydrolase gene (phnA) encodes a novel carbon-phosphorus bond cleavage enzyme whose expression is independent of the phosphate status of the cell. Analysis of the regions adjacent to the phosphonoacetate hydrolase structural gene (phnA) indicated the presence of five open reading frames (ORFs). These include one (phnR) whose putative product shows high levels of homology to the LysR family of positive transcriptional regulators. Its presence was shown to be necessary for induction of the hydrolase activity. 2-Phosphonopropionate was found to be an inducer (and poor substrate) for phosphonoacetate hydrolase. Unlike phosphonoacetate, which is also an inducer of phosphonoacetate hydrolase, entry of 2-phosphonopropionate into cells appeared to be dependent on the presence of a gene (phnB) that lies immediately downstream of phnA and whose putative product shows homology to the glycerol-3-phosphate transporter. RNA analysis revealed transcripts for the phnAB andphnR operons, which are transcribed divergently; the resulting mRNAs overlapped by 29 nucleotide bases at their 5′ ends. Transcripts of phnAB were detected only in cells grown in the presence of phosphonoacetate, whereas transcripts ofphnR were observed in cells grown under both induced and uninduced conditions. The expression of three additional genes found in the phnA region did not appear necessary for the degradation of phosphonoacetate and 2-phosphonopropionate by eitherPseudomonas putida or Escherichia colicells.

scholarly journals Identification of Differences in Genome Content among phlD-Positive Pseudomonas fluorescens Strains by Using PCR-Based Subtractive Hybridization

2002 ◽  
Vol 68 (10) ◽  
pp. 5170-5176 ◽  
Author(s):  
D. V. Mavrodi ◽  
O. V. Mavrodi ◽  
B. B. McSpadden-Gardener ◽  
B. B. Landa ◽  
D. M. Weller ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Subtractive Hybridization ◽  
Open Reading Frames ◽  
Regulatory Proteins ◽  
Rhizosphere Competence ◽  
Colicin M ◽  
Genome Content ◽  
Significant Match ◽  
Reading Frames

ABSTRACT Certain 2,4-diacetylphloroglucinol-producing strains of Pseudomonas fluorescens colonize roots and suppress soilborne diseases more effectively than others from which they are otherwise phenotypically almost indistinguishable. We recovered DNA fragments present in the superior colonizer P. fluorescens Q8r1-96 but not in the less rhizosphere-competent strain Q2-87. Of the open reading frames in 32 independent Q8r1-96-specific clones, 1 was similar to colicin M from Escherichia coli, 3 resembled known regulatory proteins, and 28 had no significant match with sequences of known function. Seven clones hybridized preferentially to DNA from strains with superior rhizosphere competence, and sequences in two others were highly expressed in vitro and in the rhizosphere.

scholarly journals Genetic Analysis of the AdnA Regulon in Pseudomonas fluorescens: Nonessential Role of Flagella in Adhesion to Sand and Biofilm Formation

2003 ◽  
Vol 185 (2) ◽  
pp. 453-460 ◽  
Author(s):  
Eduardo A. Robleto ◽  
Inmaculada López-Hernández ◽  
Mark W. Silby ◽  
Stuart B. Levy
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Transcription Factor ◽  
Pseudomonas Fluorescens ◽  
Biofilm Formation ◽  
Deletion Mutant ◽  
Open Reading Frames ◽  
Cell Processes ◽  
Reading Frames ◽  
Insertion Mutants

ABSTRACT AdnA is a transcription factor in Pseudomonas fluorescens that affects flagellar synthesis, biofilm formation, and sand adhesion. To identify the AdnA regulon, we used a promoterless Tn5-lacZ element to study the phenotypes of insertion mutants in the presence and absence of AdnA. Of 12,000 insertions, we identified seven different putative open reading frames (ORFs) activated by AdnA (named aba for activated by AdnA). aba120 and aba177 showed homology to flgC and flgI, components of the basal body of the flagella in Pseudomonas aeruginosa. Two other insertions, aba18 and aba51, disrupted genes affecting chemotaxis. The mutant loci aba160 (possibly affecting lipopolysaccharide synthesis) and aba175 (unknown function) led to loss of flagella. The mutant bearing aba203 became motile when complemented with adnA, but the mutated gene showed no similarity to known genes. Curiously, aba18, aba51, aba160, and aba203 mutants formed biofilms even in the absence of AdnA, suppressing the phenotype of the adnA deletion mutant. The combined findings suggest that flagella are nonessential for sand attachment or biofilm formation. Sequence and promoter analyses indicate that AdnA affects at least 23 ORFs either directly or by polar effects. These results support the concept that AdnA regulates cell processes other than those directly related to flagellar synthesis and define a broader cadre of genes in P. fluorescens than that described so far for its homolog, FleQ, in P. aeruginosa.

scholarly journals Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in Pseudomonas fluorescens ACB

2008 ◽  
Vol 190 (15) ◽  
pp. 5190-5198 ◽  
Author(s):  
Mariëlle J. H. Moonen ◽  
Nanne M. Kamerbeek ◽  
Adrie H. Westphal ◽  
Sjef A. Boeren ◽  
Dick B. Janssen ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Efflux Pump ◽  
Intermediate Formation ◽  
Open Reading Frames ◽  
Ring Cleavage ◽  
Semialdehyde Dehydrogenase ◽  
Genes Encoding ◽  
Intradiol Dioxygenase ◽  
Extradiol Dioxygenases ◽  
Reading Frames

ABSTRACT The catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB is known to proceed through the intermediate formation of hydroquinone. Here, we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to β-ketoadipate. The P. fluorescens ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of a 15-kb DNA fragment showed the presence of 14 open reading frames containing a gene cluster (hapCDEFGHIBA) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (hapA), 4-hydroxyphenyl acetate hydrolase (hapB), 4-hydroxymuconic semialdehyde dehydrogenase (hapE), and maleylacetate reductase (hapF). In between hapF and hapB, three genes encoding a putative intradiol dioxygenase (hapG), a protein of the Yci1 family (hapH), and a [2Fe-2S] ferredoxin (hapI) were found. Downstream of the hap genes, five open reading frames are situated encoding three putative regulatory proteins (orf10, orf12, and orf13) and two proteins possibly involved in a membrane efflux pump (orf11 and orf14). Upstream of hapE, two genes (hapC and hapD) were present that showed weak similarity with several iron(II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence, it is proposed that the hapC and hapD gene products are involved in the ring cleavage of hydroquinone.

scholarly journals A HilA-Independent Pathway to Salmonella typhimurium Invasion Gene Transcription

1999 ◽  
Vol 181 (10) ◽  
pp. 3096-3104 ◽  
Author(s):  
Jennifer L. Rakeman ◽  
Heather R. Bonifield ◽  
Samuel I. Miller
Keyword(s):  
Salmonella Typhimurium ◽  
Gene Transcription ◽  
Type Iii Secretion ◽  
Transcriptional Regulators ◽  
Open Reading Frames ◽  
Environmental Signals ◽  
Lipopolysaccharide Biosynthesis ◽  
And Function ◽  
Reading Frames ◽  
Maximal Expression

ABSTRACT Salmonella typhimurium invasion of nonphagocytic cells requires the expression of a type III secretion system (TTSS) encoded within Salmonella pathogenicity island 1 (SPI1). TTSS gene transcription is activated in response to environmental signals and requires transcriptional regulators encoded within (HilA) and outside (SirA) SPI1. Two unique loci, sirB and sirC, which contribute to SPI1 gene transcription were defined.sirC is an SPI1-encoded transcription factor of the AraC family that contributes to the invasive phenotype. sirB is required for maximal expression of sirC and consists of two open reading frames located near kdsA, a gene involved in lipopolysaccharide biosynthesis. sirC expression, unlike expression of other SPI1 genes, does not require HilA. Overexpression of sirC or sirA restores expression of a subset of SPI1 genes, including invF and sspC, in the absence of HilA. These data define roles for SirC and SirA as part of a HilA-independent pathway to SPI1 gene expression. We postulate that HilA-independent activation of inv expression is important for efficient assembly and function of the SPI1 TTSS.

The Purification and Properties of Phosphonoacetate Hydrolase, a Novel Carbon-Phosphorus Bond-Cleavage Enzyme from Pseudomonas Fluorescens 23F

1995 ◽  
Vol 234 (1) ◽  
pp. 225-230 ◽  
Author(s):  
John W. McGrath ◽  
G. Brian Wisdom ◽  
Geoffrey McMullan ◽  
Michael J. Larkin ◽  
John P. Quinn
Keyword(s):  
Pseudomonas Fluorescens ◽  
Bond Cleavage ◽  
Purification And Properties ◽  
Cleavage Enzyme

Transcript analysis of 203 novel genes from Saccharomyces cerevisiae in hap1 and rox1 mutant backgrounds

Genome ◽  
2000 ◽  
Vol 43 (5) ◽  
pp. 881-886 ◽  
Author(s):  
L J Lombardía ◽  
J L Cadahía-Rodríguez ◽  
M A Freire-Picos ◽  
M I González-Siso ◽  
A M Rodríguez-Torres ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcriptional Regulators ◽  
Open Reading Frames ◽  
Transcript Analysis ◽  
Wild Type ◽  
Aerobic Conditions ◽  
The Family ◽  
Reading Frames ◽  
Regulatory Sites

Hap1 and Rox1 are transcriptional regulators that bind regulatory sites in the promoters of oxygen-regulated genes in Saccharomyces cerevisiae. Hap1 is a heme-responsive activator of genes induced in aerobic conditions and Rox1 is a repressor of hypoxic genes in aerobic conditions. We have studied transcriptional regulation of a pool of 203 open reading frames (ORFs) from chromosomes IV, VII, and XIV in wild-type, hap1, and rox1 mutant genetic backgrounds in an attempt to extend the family of oxygen and heme regulated genes. Only three ORFs are significantly repressed by Rox1 but they cannot be considered as typical hypoxic genes because they are not overexpressed during hypoxia.Key words: Saccharomyces cerevisiae, genome analysis, chromosomes IV, VII, and XIV, gene expression, ROX1 and HAP1.

scholarly journals A Gene System for Glucitol Transport and Metabolism in Clostridium beijerinckii NCIMB 8052

1998 ◽  
Vol 64 (5) ◽  
pp. 1612-1619 ◽  
Author(s):  
Martin Tangney ◽  
John K. Brehm ◽  
Nigel P. Minton ◽  
Wilfrid J. Mitchell
Keyword(s):  
Escherichia Coli ◽  
Culture Medium ◽  
Clostridium Beijerinckii ◽  
Open Reading Frames ◽  
Chromosomal Dna ◽  
Phosphotransferase System ◽  
E Coli ◽  
Rna Analysis ◽  
Dna Fragment ◽  
Reading Frames

ABSTRACT The gutD gene of Clostridium beijerinckiiNCIMB 8052 encoding glucitol 6-phosphate dehydrogenase was cloned on a 5.7-kbp chromosomal DNA fragment by complementing an Escherichia coli gutD mutant strain and selecting for growth on glucitol. Five open reading frames (ORFs) in the order gutA1 gutA2 orfX gutB gutD were identified in a 4.0-kbp region of the cloned DNA. The deduced products of four of these ORFs were homologous to components of the glucitol phosphotransferase system (PTS) and glucitol 6-phosphate dehydrogenase from E. coli, while the remaining ORF (orfX) encoded an enzyme which had similarities to members of a family of transaldolases. A strain in which gutD was inactivated by targeted integration lacked glucitol 6-phosphate dehydrogenase activity. The gutA1 andgutA2 genes encoded two polypeptides forming enzyme IIBC of the glucitol PTS comprising three domains in the order CBC. Domain IIA of the glucitol PTS was encoded by gutB. Glucitol phosphorylation assays in which soluble and membrane fractions of cells grown on glucose (which did not synthesize the glucitol PTS) or cells grown on glucitol were used confirmed that there is a separate, soluble, glucitol-specific PTS component, which is the product of thegutB gene. The gut genes were regulated at the level of transcription and were induced in the presence of glucitol. Cells grown in the presence of glucose and glucitol utilized glucose preferentially. Following depletion of glucose, the glucitol PTS and glucitol 6-phosphate dehydrogenase were synthesized, and glucitol was removed from the culture medium. RNA analysis showed that thegut genes were not expressed until glucose was depleted.

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