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ABSTRACT:
PROVIDER: PRJNA691155 | ENA |
REPOSITORIES: ENA
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Project description:Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, -glucosidases, endoxylanases, -xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.
2016-05-02 | PXD003844 | Pride
Project description:Adaptation to public goods cheats in Pseudomonas aeruginosa
| PRJEB17843 | ENA
Project description:This study compares growth of Ruminococcus flavefaciens FD-1 with cellulose or cellobiose as the carbohydrate substrate. Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application to improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels. These results show that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components. 1 species (Ruminococcus flavefaciens FD_1), 2 conditions (cellulose, cellobiose), 4 biological replicates. Direct design with biological dye swap.
2010-05-16 | E-GEOD-15916 | biostudies-arrayexpress
Project description:Synthetic cellulolytic microbial consortia Genome sequencing
| PRJNA344818 | ENA
Project description:The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), mtr23B knockout strain (Δmtr23B) and complemented strain (Rmtr23B) on Vogel’s medium with 2% glucose (G) or 1% wheat bran and 1% cellulose (CW) as carbon resources. When cultivated in a repression medium for cellulolytic enzyme formation (G), the deletion of mtr23B upregulated genes involved in lyase activity, hydrolase activity, acyl carrier activity, monooxygenase activity, electron transfer activity, phosphopantetheine binding, heme binding, cell wall organization or biogenesis, oxidation-reduction process and extracellular region. The downregulated genes in Δmtr23B were mainly involved in transmembrane transporter activity, amino acid transmembrane transporter activity, membrane and integral component of membrane. When cultivated in an inducing medium for cellulolytic enzyme formation (CW), the downregulated genes in Δmtr23B were mainly involved in glucosidase activity, polygalacturonase activity, oxidoreductase activity, heme binding, oxidareductase activity, xylanase activity, cellulase activity, cellulose binding, oxidation-reduction process, cellulose catabolic process, xylan catabolic process and extracellular region. We find the expression levels of five secondary metabolism gene clusters (totally 28 clusters) were silenced in Δmtr23B. This study provides the information that mtr23B is required in conidiation and hydrolase activity of P. oxalicum.
2019-12-14 | GSE142001 | GEO
Project description:Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes found in viruses, archaea, bacteria as well as eukaryotes, such as fungi, algae and insects, actively contributing to the degradation of different polysaccharides. Analysis of the extracellular proteome (secretome) from Aspergillus nidulans growing in Avicel, sugarcane bagasse and sugarcane straw and analysed by LC-MS/MS in a LTQ Orbitrap Velos revealed that up to five LPMOs from family AA9 (AnLPMO9s), along with an AA3 cellobiose dehydrogenase (AnCDH1), are co-secreted upon growth on crystalline cellulose and lignocellulosic substrates, indicating their role in the degradation of plant cell wall components. Functional analysis revealed that the three main secreted LPMO9s (AnLPMO9C, AnLPMO9F and AnLPMO9G) correspond to cellulose- active enzymes with distinct regioselectivity. Deletion and overexpression studies confirmed that the abundantly secreted AnLPMO9F is a major component of the extracellular cellulolytic system, while AnLPMO9G, less abundant in the secretome, and has an important role by oxidizing crystalline fractions of cellulose. Single or double deletion of these AnLPMO9s partially impair fungal growth on sugarcane straw but not on crystalline cellulose, demonstrating the importance of LPMO9s for the saprophytic fungal lifestyle in the degradation of complex lignocellulosic substrates. Although the deletion of AnCDH1 slightly reduced the cellulolytic activity, it did not affect fungal growth indicating the existence of other electron donors to LPMOs. Additionally, double or triple knockouts of these enzymes had no accumulative deleterious effect on the cellulolytic activity nor on fungal growth, regardless of the deleted gene. Overexpression of AnLPMO9s in a cellulose-induced secretome background confirmed the importance and applicability of AnLPMO9G to improve lignocellulose saccharification.
2022-05-09 | PXD031886 | Pride
Project description:Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes found in viruses, archaea, bacteria as well as eukaryotes, such as fungi, algae and insects, actively contributing to the degradation of different polysaccharides. In Aspergillus nidulans, LPMOs from family AA9 (AnLPMO9s), along with an AA3 cellobiose dehydrogenase (AnCDH1), are co-secreted upon growth on crystalline cellulose and lignocellulosic substrates, indicating their role in the degradation of plant cell wall components. Functional analysis revealed that the three main secreted LPMO9s (AnLPMO9C, AnLPMO9F and AnLPMO9G) correspond to cellulose- active enzymes with distinct regioselectivity. Deletion and overexpression studies confirmed that the abundantly secreted AnLPMO9F is a major component of the extracellular cellulolytic system, while AnLPMO9G, less abundant in the secretome, has an important role by oxidizing crystalline fractions of cellulose. Single or double deletion of these AnLPMO9s partially impair fungal growth on sugarcane straw but not on crystalline cellulose, demonstrating the importance of LPMO9s for the saprophytic fungal lifestyle in the degradation of complex lignocellulosic substrates. Although the deletion of AnCDH1 slightly reduced the cellulolytic activity, it did not affect fungal growth indicating the existence of other electron donors to LPMOs. Additionally, double or triple knockouts of these enzymes had no accumulative deleterious effect on the cellulolytic activity nor on fungal growth, regardless of the deleted gene. The extracelllular proteomes of single deleted mutants growing in Avicel was analysed on a Q-TOF mass spectrometer and revealed an overall reduction in cellulase secretion, and some specifically some changes in the secretion of some enzymes, suggesting an adaptive mechanism adopted to compensate LPMO9s absence during cellulose degradation. Overexpression of AnLPMO9s in a cellulose-induced secretome background confirmed the importance and applicability of AnLPMO9G to improve lignocellulose saccharification.
2022-05-09 | PXD031881 | Pride