The methylcitric acid pathway in Ralstonia eutropha: new genes identified involved in propionate metabolism The GenBank accession numbers for the nucleotide sequences of the prp gene cluster are AF325554 and AF331923.

Brämer, Christian O; Steinbüchel, Alexander

doi:10.1099/00221287-147-8-2203

Cited by 70 publications

(73 citation statements)

References 51 publications

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“…R. eutropha H16 is able to bypass coenzyme B 12 -dependent reactions. It catabolizes, for example, propionyl-CoA via the methylcitric acid cycle instead of the methylmalonyl-CoA pathway 29 .…”

Section: Aerobic and Anaerobic Respirationmentioning

confidence: 99%

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

et al. 2006

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Section: Aerobic and Anaerobic Respirationmentioning

confidence: 99%

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

et al. 2006

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“…PDH1 is a homolog of a bacterial dehydratase that preferentially utilizes 2-methyl citrate, rather than citrate, in the first step of the aconitase reaction, forming 2-methyl cisaconitate (61,62). All three genes are also highly glucoserepressed (Table IV).…”

Section: Figmentioning

confidence: 99%

Multiple Pathways Are Co-regulated by the Protein Kinase Snf1 and the Transcription Factors Adr1 and Cat8

Young¹,

Dombek²,

Tachibana

et al. 2003

Journal of Biological Chemistry

255

310

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ADR1 and CAT8 encode carbon source-responsive transcriptional regulators that cooperatively control expression of genes involved in ethanol utilization. These transcription factors are active only after the diauxic transition, when glucose is depleted and energy-generating metabolism has shifted to the aerobic oxidation of non-fermentable carbon sources. The Snf1 protein kinase complex is required for activation of their downstream target genes described previously. Using DNA microarrays, we determined the extent to which these three factors collaborate in regulating the expression of the yeast genome after glucose depletion. The expression of 108 genes is significantly decreased in the absence of ADR1. The importance of ADR1 during the diauxic transition is illustrated by the observation that expression of almost one-half of the 40 most highly glucose-repressed genes is ADR1-dependent. ADR1-dependent genes fall into a variety of functional classes with carbon metabolism containing the largest number of members. Most of the genes in this class are involved in the oxidation of different non-fermentable carbon sources. These microarray data show that ADR1 coordinates the biochemical pathways that generate acetylCoA and NADH from non-fermentable substrates. Only a small number of ADR1-dependent genes are also CAT8-dependent. However, nearly one-half of the ADR1-dependent genes are also dependent on the Snf1 protein kinase for derepression. Many more genes are SNF1-dependent than are either ADR1-or CAT8-dependent suggesting that SNF1 plays a broader role in gene expression than either ADR1 or CAT8. The largest class of SNF1-dependent genes encodes regulatory proteins that could extend SNF1 dependence to additional pathways.During the diauxic shift, when yeast cells deplete the glucose in the medium, the flow of metabolites changes dramatically to adapt to the use of alternative energy and carbon sources, primarily ethanol produced during fermentation. The changes in gene expression that are required for this metabolic reorganization were dramatically revealed by DNA microarray analysis (1). The expression of more than one-quarter of the yeast genome is altered when glucose is exhausted. These alterations allow the cell to utilize carbon sources other than glucose to channel metabolites into the tricarboxylic acid and glyoxylate cycles to generate energy and synthesize intermediates for gluconeogenesis. In addition, these changes allow the cell to alter its growth rate and prepare for growth arrest and stationary phase.Numerous transcription factors and regulatory proteins are responsible for the altered transcriptional program that accompanies the depletion of glucose. Two transcription factors that play important roles during the diauxic transition are Adr1 1 and Cat8.

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“…The confirmed function of this pathway (in other organisms) is in propionate and levulinate degradation (Vagelos, 1959;Brämer and Steinbü chel, 2001). We tested for growth of M. mobilis on propionate, methyl-propionate, MCA or levulinic acid, as described in 'Materials and methods', but obtained negative results.…”

Section: Oxidation Linked To Denitrificationmentioning

confidence: 99%

Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed through transcriptomics

et al. 2009

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Methylotrophs, organisms able to gain energy and carbon from compounds containing no carboncarbon bonds, such as methane, methanol and methylated amines, are widespread in nature. However, knowledge of their nutrient preference and their metabolism is mostly based on experiments with cultures grown in defined laboratory conditions. Here, we use transcriptomics to explore the activity of one methylotroph, Methyotenera mobilis in its natural environment, lake sediment from which it has been previously isolated. Cells encapsulated in incubation cassettes were exposed to sediment conditions, with or without supplementation with a carbon/energy source (methylamine), and gene-expression patterns were compared for those cells to patterns for cells incubated in a defined medium supplemented with methylamine. A few specific trends in gene expression were observed at in situ conditions that may be of environmental significance, as follows. Expression of genes for the linear formaldehyde oxidation pathway linked to tetrahydromethanopterin increased, suggesting an important role for this pathway in situ, in contrast to laboratory condition culture, in which the cyclic ribulose monophosphate pathway seemed to be the major route for formaldehyde oxidation. Along with the ribulose monophosphate cycle that is also a major pathway for assimilating C 1 units, the methylcitric acid cycle seemd to be important in situ, suggesting that multicarbon compounds may be the natural carbon and/or energy substrates for M. mobilis, challenging the notion of an obligately methylotrophic lifestyle for this bacterium. We also detected a major switch in expression of genes responsible for the mode of motility between different conditions: from flagellum-enabled motility in defined medium to in situ expression of pili known to be involved in twitching motility and adherence. Overall, this study offers a novel approach for gaining insights into the lifestyle of individual microbes in their native environments.

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The methylcitric acid pathway in Ralstonia eutropha: new genes identified involved in propionate metabolism The GenBank accession numbers for the nucleotide sequences of the prp gene cluster are AF325554 and AF331923.

Cited by 70 publications

References 51 publications

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

Multiple Pathways Are Co-regulated by the Protein Kinase Snf1 and the Transcription Factors Adr1 and Cat8

Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed through transcriptomics

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