Lignin degradation genes studies in aquatic environment
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PROVIDER: PRJNA510500 | ENA |
REPOSITORIES: ENA
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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
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Project description:The aquatic midge, Chironomus tentans, is a keystone species in aquatic ecosystem and used as a model organism to assess chemicals toxicity in aquatic environment. To characterize midge’s cellular and molecular responses to pesticides, we established cDNA library with 10,000 cDNA elements representing 2,456 C. tentans unique genes. Blast2go identified 49 genes potentially involved in xenobiotics metabolism, including 24 cytochrome p450s (CYPs), 14 esterases (ESTs) and 11 glutathione-s-transferases (GSTs). Based on 2,456 unique genes, a cDNA microarray was developed to monitor gene expression profiles in 4th instar larvae under chlopyrifos (0.1 µg/L and 0.5 µg/L) and 1000 µg/L atrazine 48-hr exposure. We identified 149, 435 and 244 genes were significantly differentially expressed (p-value ≤0.05 with expression ratios ≥2.0) after 0.1 µg/L, 0.5 µg/L chlopyrifos, and 1000 µg/L atrazine application, respectively. Sixteen insect detoxification genes (11 CYPs, 3 GSTs and 2 esterases) were validated by qPCR and their expressions were significantly either up- or down-regulated under chlorpyrifos and atrazine exposure, especially the expression of 10 CYPs were significantly induced after chlopyrifos and atrazine exposure. The up-regulated CYPs might be involved in xenobiotic activation and/or degradation. Furthermore, we also found 5 differentially expressed hemoglobin genes. The expression changes of hemoglobins might be an adaption mechanism of C. tentans to hypoxic condition caused by xenobiotic exposure. This study provides a platform for further functional studies of pesticide-insect interactions in C. tentans.
2016-09-29 | GSE87442 | GEO
Project description:Microarrays have become established tools for describing microbial systems, however the assessment of expression profiles for environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. Thus, we apply a signal amplification approach, rather than template amplification, to analyze the expression of selected lignin-degrading enzymes in soil. Controls in the form of known amplicons and cDNA from Phanerochaete chrysosporium were included and mixed with the soil cDNA both before and after the signal amplification in order to assess the dynamic range of the microarray. We demonstrate that restored prairie soil expresses a diverse range of lignin-degrading enzymes following incubation with lignin substrate, while farmed agricultural soil does not. The mixed additions of control cDNA with soil cDNA indicate that the mixed biomass in the soil does interfere with low abundance transcript changes, nevertheless our microarray approach consistently reports the most robust signals. Keywords: comparative analysis, microbial ecology, soil microbial communities We used lignin degradation as a model process to demonstrate the use of an oligonucleotide microarray for directly detecting gene expression in soil communities using signal amplification instead of template amplification to avoid the introduction of PCR bias. In the current study, we analyzed mRNA isolated from two distinct soil microbial communities and demonstrate our ability to detect the expression of a small subset of lignin degrading genes following exposure to a lignitic substrate. We also included purified control amplicons and mixed target experiments with pure P. chrysosporium genomic cDNA to determine the level of interference from soil biomass on target hybridization.
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