A Set of Activators and Repressors Control Peripheral Glucose Pathways in
            <i>Pseudomonas putida</i>
            To Yield a Common Central Intermediate

Castillo, Teresa del; Duque, Estrella; Ramos, Juan L.

doi:10.1128/jb.01726-07

Cited by 86 publications

(91 citation statements)

References 45 publications

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“…First, both synonymous mutations occur in a gene predicted to encode a permease subunit of an ABC transporter, and homologues of this transport system in P. aeruginosa and P. putida are glucose inducible and responsible for glucose uptake ( Fig. 2) [21][22][23][24] . Second, the benefits conferred are specific to glucose: neither mutation significantly affected fitness on alternate sugars (Fig.…”

Section: Resultsmentioning

confidence: 99%

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

2014

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Conventional wisdom holds that synonymous mutations, nucleotide changes that do not alter the encoded amino acid, have no detectable effect on phenotype or fitness. However, a growing body of evidence from both comparative and experimental studies suggests otherwise. Synonymous mutations have been shown to impact gene expression, protein folding and fitness, however, direct evidence that they can be positively selected, and so contribute to adaptation, is lacking. Here we report the recovery of two beneficial synonymous single base pair changes that arose spontaneously and independently in an experimentally evolved population of Pseudomonas fluorescens. We show experimentally that these mutations increase fitness by an amount comparable to non-synonymous mutations and that the fitness increases stem from increased gene expression. These results provide unequivocal evidence that synonymous mutations can drive adaptive evolution and suggest that this class of mutation may be underappreciated as a cause of adaptation and evolutionary dynamics.

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Section: Resultsmentioning

confidence: 99%

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

2014

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“…In Pseudomonas, the inner membrane glucose transport component has not yet been identified; however, a specific transport component has been studied in detail for maltose uptake in E. coli (Chen et al, 2001). The downregulation of genes involved in the glucose uptake during growth on glucose and toluene was observed in P. putida KT2440 which can allow the uptake of glucose via the oxidative and phosphorylative pathway (del Castillo & Ramos, 2007;del Castillo et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

Repression of the glucose-inducible outer-membrane protein OprB during utilization of aromatic compounds and organic acids in Pseudomonas putida CSV86

et al. 2011

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Pseudomonas putida CSV86 shows preferential utilization of aromatic compounds over glucose. Protein analysis and [ 14 C]glucose-binding studies of the outer membrane fraction of cells grown on different carbon sources revealed a 40 kDa protein that was transcriptionally induced by glucose and repressed by aromatics and succinate. Based on 2D gel electrophoresis and liquid chromatography-tandem mass spectrometry analysis, the 40 kDa protein closely resembled the porin B of P. putida KT2440 and carbohydrate-selective porin OprB of various Pseudomonas strains. The purified native protein (i) was estimated to be a homotrimer of 125 kDa with a subunit molecular mass of 40 kDa, (ii) displayed heat modifiability of electrophoretic mobility, (iii) showed channel conductance of 166 pS in 1 M KCl, (iv) permeated various sugars (mono-, di-and trisaccharides), organic acids, amino acids and aromatic compounds, and (v) harboured a glucosespecific and saturable binding site with a dissociation constant of 1.3 mM. These results identify the glucose-inducible outer-membrane protein of P. putida CSV86 as a carbohydrate-selective protein OprB. Besides modulation of intracellular glucose-metabolizing enzymes and specific glucose-binding periplasmic space protein, the repression of OprB by aromatics and organic acids, even in the presence of glucose, also contributes significantly to the strain's ability to utilize aromatics and organic acids over glucose.

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“…del Castillo et al (11,13) showed that all sequenced Pseudomonas sp. genomes exhibit the same physical organization of the zwf/edd/pgl and eda/glk operons, with the hexR gene being transcribed divergently with respect to the edd promoter.…”

Section: Discussionmentioning

confidence: 99%

“…Glucose catabolic pathways in P. putida. The figure is modified from that in del Castillo et al (11,13) and del Castillo and Ramos (12) Glk, glucokinase; Zwf, glucose 6-P dehydrogenase; Pgl, 6-phosphogluconolactonase; Edd, 6-phosphogluconate dehydratase; Gcd, glucose dehydrogenase; Gad, gluconate oxidase; KguK, 2-ketogluconate kinase; KguD, 2-ketogluconate-6-phosphate dehydrogenase; G3P, glyceraldehyde 3-phosphate; Pyr, pyruvate; GnuK, gluconate kinase. FIGURE 2.…”

Section: Bacterial Strains and Plasmids Used In This Study-mentioning

confidence: 99%

“…The two described operons and the gap-1 gene are all induced in cells growing with glucose, gluconate, and 2-ketogluconate, whereas the level of expression of hexR does not vary significantly regardless of the carbon source used for growth (13,23). It should be noted that due to the physical and transcriptional organization of the two operons that transcribe glucokinase pathway genes (glk, zwf, and pgl), the regulator of the glucose transport system (gltR2), and the Entner-Doudoroff pathway genes (edd, eda), glucokinase pathway genes are cotranscribed with Entner-Doudoroff pathway enzymes.…”

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Regulation of Glucose Metabolism in Pseudomonas

Daddaoua

Krell

Ramos

2009

Journal of Biological Chemistry

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In Pseudomonas putida, genes for the glucose phosphorylative pathway and the Entner-Doudoroff pathway are organized in two operons; one made up of the zwf, pgl, and eda genes and another consisting of the edd, glk, gltR2, and gltS genes. Divergently with respect to the edd gene is the gap-1 gene. Expression from P zwf , P edd , and P gap is modulated by HexR in response to the availability of glucose in the medium. To study the regulatory process in greater detail we purified HexR and showed that it is a monomer in solution. Electrophoretic mobility shift assays and isothermal titration calorimetry assays were done showing that HexR recognizes the P edd , P zwf , and P gap-1 promoters with affinity in the nanomolar range. DNA footprinting assays identified the binding site between ؉30 and ؉1 at P zwf , between ؉16 and ؉41 at P edd , and between ؊6 and ؉18 at P gap-1 . Based on DNA sequence alignment of the target sites and isothermal titration calorimetry data, two monomers of HexR bind to a pseudopalindrome with a consensus sequence of 5-TTGTN 7-8 ACAA-3. Binding of the Entner-Doudoroff pathway intermediate 2-keto-3-deoxy-6-phosphogluconate to HexR released the repressor from its target operators, whereas other chemicals such as glucose, glucose 6-phosphate, and 6-phosphogluconate did not induce complex dissociation. The phosphorylated effector is likely to be recognized by a sugar isomerase domain located at the C-terminal end of HexR, whereas the helix-turn-helix DNA binding domain of HexR exhibits high similarity to proteins of the RpiR family of regulators.Bacteria of the genus Pseudomonas are ubiquitous inhabitants of soil, water, plant surfaces, and animal tissues. The complete genome sequences of a number of Pseudomonas species and different strains have been deciphered, and their analysis has revealed that Pseudomonas exhibits a limited ability to metabolize sugars; nonetheless, the genomes of all Pseudomonas strains sequenced to date show that they possess the necessary genetic information to metabolize glucose (1-8). In fact, glucose metabolism in Pseudomonas is biochemically rich, as up to three convergent pathways that transform the sugar into 6-phosphogluconate have been described. Subsequently, 6-phosphogluconate is metabolized by Entner-Doudoroff enzymes into central metabolites (9 -13).Glucose metabolism is compartmentalized in Pseudomonas in the sense that once glucose passes the outer membrane through the OprB porin and reaches the periplasm (14 -16), it can be transported to the cytoplasm, or it can be oxidized by the action of the periplasmic glucose dehydrogenase to yield gluconate, which by the action of gluconate dehydrogenase is transformed into 2-ketogluconate. Gluconate and 2-ketogluconate may also be transported to the cytoplasm through a process mediated by the GnuK and KguP transporters, respectively. In the cytoplasm gluconate is directly phosphorylated to 6-phosphogluconate, whereas two reactions mediated by KguK and KguD are needed to convert 2-ketogluconate into 6-phosphoglucona...

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A Set of Activators and Repressors Control Peripheral Glucose Pathways in Pseudomonas putida To Yield a Common Central Intermediate

Cited by 86 publications

References 45 publications

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

Repression of the glucose-inducible outer-membrane protein OprB during utilization of aromatic compounds and organic acids in Pseudomonas putida CSV86

Regulation of Glucose Metabolism in Pseudomonas

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