Bacterial strains from the Baltic sea
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PROVIDER: PRJEB21273 | ENA |
REPOSITORIES: ENA
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Project description:iJN1462 (i) incorporates several hundred additional genes and associated reactions resulting in new predictive capabilities, including new nutrients supporting growth; (ii) was validated by in vivo growth screens that included previously untested carbon (48) and nitrogen (41) sources; (iii) yielded gene essentiality predictions showing large accuracy when compared with a knock-out library and Bar-seq data; and (iv) allowed mapping of its network to 82 P. putida sequenced strains revealing functional core that reflect the large metabolic versatility of this species, including aromatic compounds derived from lignin.
2022-04-25 | MODEL2204040001 | BioModels
Project description:We evaluated the possible mechanisms by which exposures to pulp and paper mill effluents gene expression in the fathead minnow hypothalamus Keywords: Toxicology Sexually mature fathead minnows were exposed to 100% pulp and paper mill effluents for 5 days. Tanks contained 4 females and 2 males. A total 4 tanks per effluents were used in this experiment. TM5, TM6, and KM4 represent different pulp and paper mill effluents from different mills coded for by FPInnovations-Paprican.
2010-07-07 | E-GEOD-17130 | biostudies-arrayexpress
Project description:Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in Nature. While lignin depolymerization by WRF has been exhaustively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here we employ 13C-labeling and systems biology approaches to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems, and furthermore establishes a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts – a key step towards enabling a sustainable bioeconomy.
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Project description:paper pulp sludge enviromental metagenome
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2021-05-22 | GSE174697 | GEO
Project description:White-rot fungi (WRF), considered the most efficient organisms at degrading organic carbon in the biosphere, are found in plant cell wall lignin biopolymer. We employ multi-omics to demonstrate that Trametes versicolor and Gelatoporia subvermispora funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems.
2021-02-10 | PXD019839 | Pride
Project description:Valencia orange (Citrus sinensis Osbeck), namely summer orange (SO), is a type of late-ripening sweet oranges, the ripening time of which is 4 to 5 months later than that of the middle-ripening common sweet orange (CO). The mastication of SO fruit pulp is worse than that of CO. To date, how the late-ripening and poor pulp mastication traits were domesticated in SO is unknown. In this study, 13 SO cultivars and 12 CO cultivars were used for whole-genome resequencing. Population genetic diversity analysis divided these 25 samples into SO and CO subgroups, respectively. There were 144 and 141 genes identified by selective sweep analysis to be strongly selected during SO and CO evolutionary processes, respectively. Based on gene functional annotation and pathway enrichment analysis, most of these selected genes in SO were related to resistance and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of the peel and pulp tissues among three SO cultivars and three CO cultivars, which also revealed the difference of lignin synthesis between SO and CO fruits. Moreover, according to the comparative analysis of the lignin content and the expressions of the genes related to lignin biosynthesis in SO and CO fruits, we suggested that lignin may play an important role in the pulp mastication trait of SO. In addition, a SNP molecular marker was developed to distinguish SO and CO. This study reveals that the mastication trait may be formed in the process of SO domestication, while the late-ripening trait may be formed in a genetic mutation event.
2021-08-26 | GSE164142 | GEO
Project description:The Trametes versicolor genome is predicted to encode many enzymes that can effectively degrade lignin, making it a has potentially useful application intool for biopulping and biobleaching. Poplar is an important and widely cultivated species of tree species, which isand extensively applied used in the pulping industry. However, the wood degradation mechanism of T. versicolor from transcriptomic level is not clear. To reveal identify the enzymes that contributeing to lignocellulose degraredauction and its degradation mechanisms, we evaluated transcriptomic how study theof T. versicolor transcriptome was changes during evaluated growthing on the poplar wood relative to growth on glucose medium. 853 genes were differentially expressed;, 360 genes were up-regulated on poplar wood, and 493 genes were down-regulated on poplar wood. Notably, most genes relative involved into lignin degradation were up-regulated, including eight lignin peroxidase (LiP) genes, and two manganese peroxidase (MnP) genes etc. Genes encoding cellulose and hemicelluloses degrading-enzymesation were mostly down-regulated, including six endo-β-1, 4-glucanase genes, three cellobiohydrolase I genes, and one cellobiohydrolase II gene, etc. MeanwhileAdditionally, expression of more significant expansion of P450s in T. versicolor genome, along with differences in carbohydrate- and lignin-degrading enzymes, could bewere correlated withto poplar wood degradation. Our results revealed transcriptomic characterizeation transcriptomic changes related toof lignocellulose degradation. Therefore, our results cwould be benuseful for the development ofefit T. versicolor as a tool to improve the efficiency of lignin degradation, and provide a theoretical foundation for a new paper pulp manufacturing processe 1,T.versicolor groewn on PDA medium. 2, T. versicolor growing on the a glucose carbon medium of glucose. 3, T. versicolor growing on poplar medium
2016-08-06 | E-GEOD-81742 | biostudies-arrayexpress
Project description:Pulp and paper mill wastewater Metagenome
| PRJNA763013 | ENA
Project description:The Trametes versicolor genome is predicted to encode many enzymes that can effectively degrade lignin, making it a has potentially useful application intool for biopulping and biobleaching. Poplar is an important and widely cultivated species of tree species, which isand extensively applied used in the pulping industry. However, the wood degradation mechanism of T. versicolor from transcriptomic level is not clear. To reveal identify the enzymes that contributeing to lignocellulose degraredauction and its degradation mechanisms, we evaluated transcriptomic how study theof T. versicolor transcriptome was changes during evaluated growthing on the poplar wood relative to growth on glucose medium. 853 genes were differentially expressed;, 360 genes were up-regulated on poplar wood, and 493 genes were down-regulated on poplar wood. Notably, most genes relative involved into lignin degradation were up-regulated, including eight lignin peroxidase (LiP) genes, and two manganese peroxidase (MnP) genes etc. Genes encoding cellulose and hemicelluloses degrading-enzymesation were mostly down-regulated, including six endo-β-1, 4-glucanase genes, three cellobiohydrolase I genes, and one cellobiohydrolase II gene, etc. MeanwhileAdditionally, expression of more significant expansion of P450s in T. versicolor genome, along with differences in carbohydrate- and lignin-degrading enzymes, could bewere correlated withto poplar wood degradation. Our results revealed transcriptomic characterizeation transcriptomic changes related toof lignocellulose degradation. Therefore, our results cwould be benuseful for the development ofefit T. versicolor as a tool to improve the efficiency of lignin degradation, and provide a theoretical foundation for a new paper pulp manufacturing processe
2016-08-06 | GSE81742 | GEO