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

Pohlmann, Anne; Fricke, W. Florian; Reinecke, Frank; Kusian, Bernhard; Liesegang, Heiko; Cramm, Rainer; Eitinger, Thomas; Ewering, Christian; Pötter, Markus; Schwartz, Edward L.; Strittmatter, Axel; Voß, Ingo; Gottschalk, Gerhard; Steinbüchel, Alexander; Friedrich, Bärbel; Bowien, Botho

doi:10.1038/nbt1244

Cited by 535 publications

(498 citation statements)

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“…The biochemical reactions were collected and analyzed from various public databases, including Kyoto Encyclopedia of Genes and Genomes (KEGG, [8]), BioSilico [9], Metacyc [10] and the University of Minnesota Biocatalyst/Biodegradation Database (UMBBD; http://umbbd.msi.umn.edu/). The transport reactions were analyzed based on TransportDB [11] and literature [1,12] as they are not sufficiently described in typical metabolic pathway databases. The individual reactions were balanced with respect to element and charge for pH 6, 7, and 8.…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…It is a lithoautotrophic bacterium that utilizes CO 2 and H 2 as sources of carbon and energy in the absence of organic substrates, and is an environmentally important bacterium that can degrade various aromatic compounds [1]. It is also the best known polyhydroxyalkanoates (PHAs) producer [1-3]. The genome of R. eutropha H16 consists of two chromosomes and one plasmid, which have been fully sequenced and annotated: chromosome1 (4,052,032 bp), chromosome 2 (2,912,490 bp) and megaplasmid pHG1 (452,156 bp) [1].…”

Section: Introductionmentioning

confidence: 99%

“…It is also the best known polyhydroxyalkanoates (PHAs) producer [1-3]. The genome of R. eutropha H16 consists of two chromosomes and one plasmid, which have been fully sequenced and annotated: chromosome1 (4,052,032 bp), chromosome 2 (2,912,490 bp) and megaplasmid pHG1 (452,156 bp) [1]. …”

Section: Introductionmentioning

confidence: 99%

“…In the absence of organic substrates, R. eutropha operates its autotrophic metabolism by fixing CO 2 via Calvin-Benson-Bassham cycle (CBB) and oxidixing H 2 , which is calatalyzed by two NiFe dehydrogenases [4]. Another significant characteristic of R. eutropha is that it can accumulate large amounts of PHA, such as poly[R-(-)-3hydroxybutyrate] (PHB) as intracellular granules of up to 90% of dry cell weight under unbalanced growth conditions [1,2,5]. For this reason, R. eutropha H16 has attracted biotechnological interest as an excellent producer of biodegradable plastics and served as a source of the PHA biosynthetic machinary for other recombinant microorganisms [6].…”

Section: Introductionmentioning

confidence: 99%

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Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

2011

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BackgroundRalstonia eutropha H16, found in both soil and water, is a Gram-negative lithoautotrophic bacterium that can utillize CO2 and H2 as its sources of carbon and energy in the absence of organic substrates. R. eutropha H16 can reach high cell densities either under lithoautotrophic or heterotrophic conditions, which makes it suitable for a number of biotechnological applications. It is the best known and most promising producer of polyhydroxyalkanoates (PHAs) from various carbon substrates and is an environmentally important bacterium that can degrade aromatic compounds. In order to make R. eutropha H16 a more efficient and robust biofactory, system-wide metabolic engineering to improve its metabolic performance is essential. Thus, it is necessary to analyze its metabolic characteristics systematically and optimize the entire metabolic network at systems level.ResultsWe present the lithoautotrophic genome-scale metabolic model of R. eutropha H16 based on the annotated genome with biochemical and physiological information. The stoichiometic model, RehMBEL1391, is composed of 1391 reactions including 229 transport reactions and 1171 metabolites. Constraints-based flux analyses were performed to refine and validate the genome-scale metabolic model under environmental and genetic perturbations. First, the lithoautotrophic growth characteristics of R. eutropha H16 were investigated under varying feeding ratios of gas mixture. Second, the genome-scale metabolic model was used to design the strategies for the production of poly[R-(-)-3hydroxybutyrate] (PHB) under different pH values and carbon/nitrogen source uptake ratios. It was also used to analyze the metabolic characteristics of R. eutropha when the phosphofructokinase gene was expressed. Finally, in silico gene knockout simulations were performed to identify targets for metabolic engineering essential for the production of 2-methylcitric acid in R. eutropha H16.ConclusionThe genome-scale metabolic model, RehMBEL1391, successfully represented metabolic characteristics of R. eutropha H16 at systems level. The reconstructed genome-scale metabolic model can be employed as an useful tool for understanding its metabolic capabilities, predicting its physiological consequences in response to various environmental and genetic changes, and developing strategies for systems metabolic engineering to improve its metabolic performance.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

2011

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Bioengineering of Polyhydroxyalkanoates

Taguchi

2017

Encyclopedia of Polymer Science and Technology

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Establishment of a renewable whole‐cell catalyst platform for the production of biobased polymeric materials is an important area of synthetic biology. In this article, the fundamental properties of natural polyesters polyhydroxyalkanoates (PHAs), bearing a structural variety of over 160 monomeric constituents, are explained especially in terms of structure and function. Based on the strategic pathway engineering, successful bioengineering of PHAs is introduced together with several case studies on monomer‐supplying routes and PHA synthase enzyme alteration. Particularly, the effectiveness of engineering PHA synthesis–related enzymes is highly stressed. Important advances, such as the discovery of a “lactate‐polymerizing enzyme” (LPE) and the establishment of microbial platform for lactate‐based polyesters from renewable feedstock, are also presented. LPE‐based achievements for creating a new variety of incorporated unnatural monomers are expanded to 2‐hydroxybutyrate and glycolate units. This is a typical synthetic biology integrated by various biotechnological toolboxes to create novel polyesters, such as LA‐based polyesters and tailored‐made PHAs.

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High‐Resolution Metagenomics: Assessing Specific Functional Types in Complex Microbial Communities

Chistoserdova

2011

Handbook of Molecular Microbial Ecology I

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

Cited by 535 publications

References 42 publications

Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

Bioengineering of Polyhydroxyalkanoates

High‐Resolution Metagenomics: Assessing Specific Functional Types in Complex Microbial Communities

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