Multivariate analysis of microarray data by principal component discriminant analysis: prioritizing relevant transcripts linked to the degradation of different carbohydrates in Pseudomonas putida S12

Werf, M.J. van der; Pieterse, Bart; Luijk, N. van; Schuren, Frank; Vat, Bianca van der Werff-van der; Overkamp, Karin; Jellema, Renger H.

doi:10.1099/mic.0.28278-0

Cited by 31 publications

(24 citation statements)

References 41 publications

(44 reference statements)

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“…Because the edd and eda gene products are the sine qua non for 6-phosphogluconate metabolism, the physical and genetic organization of the edd/glk and eda/zwf-1 genes explains why this pathway is operational in P. putida KT2440 (46).…”

Section: Discussionmentioning

confidence: 99%

Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism inPseudomonas putida: Genomic and Flux Analysis

et al. 2007

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In this study, we show that glucose catabolism in Pseudomonas putida occurs through the simultaneous operation of three pathways that converge at the level of 6-phosphogluconate, which is metabolized by the Edd and Eda Entner/Doudoroff enzymes to central metabolites. When glucose enters the periplasmic space through specific OprB porins, it can either be internalized into the cytoplasm or be oxidized to gluconate. Glucose is transported to the cytoplasm in a process mediated by an ABC uptake system encoded by open reading frames PP1015 to PP1018 and is then phosphorylated by glucokinase (encoded by the glk gene) and converted by glucose-6-phosphate dehydrogenase (encoded by the zwf genes) to 6-phosphogluconate. Gluconate in the periplasm can be transported into the cytoplasm and subsequently phosphorylated by gluconokinase to 6-phosphogluconate or oxidized to 2-ketogluconate, which is transported to the cytoplasm, and subsequently phosphorylated and reduced to 6-phosphogluconate. In the wild-type strain, glucose was consumed at a rate of around 6 mmol g ؊1 h ؊1, which allowed a growth rate of 0.58 h ؊1 and a biomass yield of 0.44 g/g carbon used. Flux analysis of 13 C-labeled glucose revealed that, in the Krebs cycle, most of the oxalacetate fraction was produced by the pyruvate shunt rather than by the direct oxidation of malate by malate dehydrogenase. Enzymatic and microarray assays revealed that the enzymes, regulators, and transport systems of the three peripheral glucose pathways were induced in response to glucose in the outer medium. We generated a series of isogenic mutants in one or more of the steps of all three pathways and found that, although all three functioned simultaneously, the glucokinase pathway and the 2-ketogluconate loop were quantitatively more important than the direct phosphorylation of gluconate. In physical terms, glucose catabolism genes were organized in a series of clusters scattered along the chromosome. Within each of the clusters, genes encoding porins, transporters, enzymes, and regulators formed operons, suggesting that genes in each cluster coevolved. The glk gene encoding glucokinase was located in an operon with the edd gene, whereas the zwf-1 gene, encoding glucose-6-phosphate dehydrogenase, formed an operon with the eda gene. Therefore, the enzymes of the glucokinase pathway and those of the Entner-Doudoroff pathway are physically linked and induced simultaneously. It can therefore be concluded that the glucokinase pathway is a sine qua non condition for P. putida to grow with glucose.

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Section: Discussionmentioning

confidence: 99%

Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism inPseudomonas putida: Genomic and Flux Analysis

et al. 2007

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“…Genes with a signal log 2 ratio of C1 or B-1 at least at one time point were classified as differentially expressed, and clustered using the self-organizing tree algorithm (SOTA) (Herrero et al 2001) and complete time-course profiles (0, 3, 6, 9, and 12 h). The number of groups was decided based on principal-component analysis (PCA; van der Werf et al 2006). Since the cumulative contribution ratio of the first three principal components was 97.5%, we subdivided the genes into three groups with different expression profiles.…”

Section: Cluster Analysismentioning

confidence: 99%

Global gene expression analysis of Aspergillus nidulans reveals metabolic shift and transcription suppression under hypoxia

et al. 2010

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Hypoxia imposes a challenge upon most filamentous fungi that require oxygen for proliferation. Here, we used whole genome DNA microarrays to investigate global transcriptional changes in Aspergillus nidulans gene expression after exposure to hypoxia followed by normoxia. Aeration affected the expression of 2,864 genes (27% of the total number of genes in the fungus), of which 50% were either induced or repressed under hypoxic conditions. Up-regulated genes included those for glycolysis, ethanol production, the tricarboxylic acid (TCA) cycle, and for the γ-aminobutyrate (GABA) shunt that bypasses two steps of the TCA cycle. Ethanol and lactate production under hypoxic conditions indicated that glucose was fermented to these compounds via the glycolytic pathway. Since the GABA shunt bypasses the NADH-generating reaction of the TCA cycle catalyzed by oxoglutarate dehydrogenase, hypoxic A. nidulans cells eliminated excess NADH. Hypoxia down-regulated some genes involved in transcription initiation by RNA polymerase II, and lowered the cellular mRNA content. These functions were resumed by re-oxygenation, indicating that A. nidulans controls global transcription to adapt to a hypoxic environment. This study is the first to show that hypoxia elicits systematic transcriptional responses in A. nidulans.

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“…Differentially expressed genes representing the complete time course profile (S0, S60, S120, S150, and ZSP) were clustered using the K-means algorithm. To discover the number of groups to be considered, we applied principal-component analysis (PCA) (38). Since the differences between successive PCA components (eigenvalues) go rapidly to near zero after the eighth component, we subdivided the genes into eight groups with different expression patterns.…”

Section: Methodsmentioning

confidence: 99%

Global Gene Expression Analysis during Sporulation of the Aquatic Fungus Blastocladiella emersonii

Vieira

Gomes

2010

Eukaryot Cell

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The Blastocladiella emersonii life cycle presents a number of drastic biochemical and morphological changes, mainly during two cell differentiation stages: germination and sporulation. To investigate the transcriptional changes taking place during the sporulation phase, which culminates with the production of the zoospores, motile cells responsible for the dispersal of the fungus, microarray experiments were performed. Among the 3,773 distinct genes investigated, a total of 1,207 were classified as differentially expressed, relative to time zero of sporulation, at at least one of the time points analyzed. These results indicate that accurate transcriptional control takes place during sporulation, as well as indicating the necessity for distinct molecular functions throughout this differentiation process. The main functional categories overrepresented among upregulated genes were those involving the microtubule, the cytoskeleton, signal transduction involving Ca 2؉ , and chromosome organization. On the other hand, protein biosynthesis, central carbon metabolism, and protein degradation were the most represented functional categories among downregulated genes. Gene expression changes were also analyzed in cells sporulating in the presence of subinhibitory concentrations of glucose or tryptophan. Data obtained revealed overexpression of microtubule and cytoskeleton transcripts in the presence of glucose, probably causing the shape and motility problems observed in the zoospores produced under this condition. In contrast, the presence of tryptophan during sporulation led to upregulation of genes involved in oxidative stress, proteolysis, and protein folding. These results indicate that distinct physiological pathways are involved in the inhibition of sporulation due to these two classes of nutrient sources.The life cycle of Blastocladiella emersonii, an aquatic fungus of the class Blastocladiomycetes, involves a series of complex morphological and biochemical events, which involve transcriptional, posttranscriptional, and posttranslational mechanisms of control, especially during two stages of cell differentiation, the germination and the sporulation of the fungus (21). Germination starts with the zoospore, a motile uninucleated wall-less nongrowing cell, which is responsible for the dispersal of the fungus. In the presence of appropriate stimuli, the zoospore germinates, undergoing a number of biochemical and morphological changes. The early events of germination, which include retraction of the single polar flagellum, construction of a cell wall rich in chitin, and cleavage of a giant mitochondrion into normal-size ones, do not require concomitant RNA and protein synthesis and involve posttranslational regulatory events (17,20,30,31,35,36). Major changes in the pattern of RNA and protein synthesis are observed only at the late events of this stage, when the germ tube begins to branch, giving rise to a rhizoidal system through which nutrients are absorbed, and when the cells enter the vegetative growth phase (17,20...

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Multivariate analysis of microarray data by principal component discriminant analysis: prioritizing relevant transcripts linked to the degradation of different carbohydrates in Pseudomonas putida S12

Cited by 31 publications

References 41 publications

Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism inPseudomonas putida: Genomic and Flux Analysis

Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism inPseudomonas putida: Genomic and Flux Analysis

Global gene expression analysis of Aspergillus nidulans reveals metabolic shift and transcription suppression under hypoxia

Global Gene Expression Analysis during Sporulation of the Aquatic Fungus Blastocladiella emersonii

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