19 documents found, page 1 of 2
FROG analysis ensures the reproducibility of genome scale metabolic models
Raman, Karthik; Kratochvil, Miroslav; Olivier, Brett G.; Konig, Matthias; Sengupta, Pratyay; Baskaran, Dinesh Kumar Kuppa; Nguyen, Tung V NGenome scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting a...
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms metabolism under different conditions1. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Geneproteinreaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with ...
Genome-guided analysis allows the identification of novel physiological traits ...
Strepis, Nikolaos; Naranjo, Henry D.; Meier-Kolthoff, Jan; Göker, Markus; Shapiro, Nicole; Kyrpides, Nikos; Klenk, Hans-Peter; Schaap, Peter J.The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly ...
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Metabolic shift induced by synthetic co-cultivation promotes high yield of chai...
Diender, Martijn; Parera Olm, Ivette; Gelderloos, Marten; Koehorst, Jasper J.; Schaap, Peter J.; Stams, Alfons Johannes Maria; Sousa, Diana Zita MachadoBio-catalytic processes for sustainable production of chemicals and fuels receive increased attention within the concept of circular economy. Strategies to improve these production processes include genetic engineering of bio-catalysts or process technological optimization. Alternatively, synthetic microbial co-cultures can be used to enhance production of chemicals of interest. It remains often unclear however...
Trichococcus species as catalysts for biotechnological production of 1,3-propan...
Strepis, Nikolaos; Koehorst, Jasper; Naranjo, Henry Benavides; Schaap, Peter J.; Stams, Alfons Johannes Maria; Sousa, Diana Zita MachadoNowadays, large amounts of waste glycerol are generated as a major byproduct from biodiesel industry. Glycerol can be converted to 1,3-propanediol (1,3-PDO), a building block for the synthesis of polyester and biodegradable plastic fibers. We have previously isolated a novel Trichococcus species, strain ES5, which is capable to anaerobically produce 1,3-PDO from glycerol, an ability it shares with Trichococcus ...
Concurrent haloalkanoate degradation and chlorate reduction by Pseudomonas chlo...
Peng, P.; Zheng, Y.; Koehorst, J. J.; Schaap, Peter J.; Stams, Alfons Johannes Maria; Smidt, H.; Atashgahi, S.Haloalkanoates are environmental pollutants that can be degraded aerobically by microorganisms producing hydrolytic dehalogenases. However, there is a lack of information about the anaerobic degradation of haloalkanoates. Genome analysis of Pseudomonas chloritidismutans AW-1T, a facultative anaerobic chloratereducing bacterium, showed the presence of two putative haloacid dehalogenase genes, the L-DEX gene and ...
Description of Trichococcus ilyis sp. nov. by combined physiological and in sil...
Strepis, Nikolaos; Sánchez-Andrea, Irene; van Gelder, Antonie H.; van Kruistum, Henri; Shapiro, Nicole; Kyrpides, Nikos; Göker, MarkusSpecies of the genus Trichococcus share high similarity of their 16S rRNA gene sequences (>99%). Digital DNADNA hybridization values (dDDH) among type strains of all described species of the genus Trichococcus ( T. flocculiformis DSM 2094T , T. pasteurii DSM 2381T , T. collinsii DSM 14526T , T. palustris DSM 9172T, and T. patagoniensis DSM 18806T) indicated that Trichococcus sp. strain R210T represents a novel ...
Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by g...
Visser, Michael; Pieterse, Mervin M.; Pinkse, Martijn W. H.; Nijsse, Bart; Verhaert, Peter D. E. M.; Vos, Willem M. de; Schaap, Peter J.The Sporomusa genus comprises anaerobic spore-forming acetogenic bacteria that stain Gram-negative. Sporomusa species typically grow with one-carbon substrates and N-methylated compounds. In the degradation of these compounds methyltransferases are involved. In addition, Sporomusa species can grow autotrophically with H2 and CO2, and use a variety of sugars for acetogenic growth. Here we describe a genome analy...
Genome and proteome analysis of Pseudomonas chloritidismutans AW-1T that grows ...
Mehboob, Farrakh; Oosterkamp, Margreet J.; Koehorst, Jasper J.; Farrakh, Sumaira; Veuskens, Teun; Plugge, Caroline M.; Boeren, Sjef; Vos, Willem M. deGrowth of Pseudomonas chloritidismutans AW-1T on C7 to C12 n-alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G+C content of 62.5% The automatic annotation identified 4767 protein-encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The disti...