RNA-seq analysis of Bacteroides xylanisolvens XB1AT grown on pectin or xylan
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ABSTRACT:
ORGANISM(S): Bacteroides xylanisolvens
SUBMITTER: Christopher Fields
PROVIDER: E-GEOD-74379 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide.
2015-10-28 | GSE74379 | GEO
Project description:Filamentous fungi are powerful producers of hydrolytic enzymes for the deconstruction of plant cell wall polysaccharides. However, the central question of how these sugars are perceived in the context of the complex cell wall matrix remains largely elusive. To address this question in a systematic fashion we performed an extensive comparative systems analysis of how the model filamentous fungus Neurospora crassa responds to the three main cell wall polysaccharides: pectin, hemicellulose and cellulose. We found the pectic response to be largely independent of the cellulolytic one with some overlap to hemicellulose, and in its extent surprisingly high, suggesting advantages for the fungus beyond being a mere carbon source. Our approach furthermore allowed us to identify carbon source-specific adaptations, such as the induction of the unfolded protein response on cellulose, and a commonly induced set of 29 genes likely involved in carbon scouting. Moreover, by hierarchical clustering we generated a co-expression matrix useful for the discovery of new components involved in polysaccharide utilization. This is exemplified by the identification of lat-1, which we demonstrate to encode for the physiologically relevant arabinose transporter in Neurospora. The analyses presented here are an important step towards understanding fungal degradation processes of complex biomass. Our data are based on carbon source transfer experiments. For this, N. crassa pregrown in sucrose for 16 hrs was washed in media without carbon and then transferred to either pectin, orange peel powder (OPP), xylan, Avicel (cellulose), sucrose, or media without carbon (NoC) for another 4 hrs. Biological triplicates (pectin, Avicel, sucrose, NoC) or duplicates (OPP) were used to identify differentially expressed genes in WT. For xylan only a single library was prepared, which was found to correlate well with previously published microarray data (Sun et al. 2012; doi: 10.1128/EC.05327-11)
2013-11-27 | E-GEOD-42692 | biostudies-arrayexpress
Project description:Hyperthermophilic bacteria of the genus Thermotoga are known to utilize a wide range of simple and complex polysaccharides. T. maritima's transcriptional response to a variety of mono- and poly-saccharides was previously studied to assign functions to genes involved in carbohydrate uptake and utilization. To compare and contrast closely-related members of the Thermotoga genus, a four-species microarray was developed by expanding a whole genome T. maritima array to include unique genes from three other species (T. neapolitana, T. petrophila, and T. sp. RQ2). This multi-species array was used to investigate the diversity of the genus, specifically the response of each of the four species to a mixture of polysaccharides (galactomannan, glucomannan, xylan, pectin, lichenan, and carboxymethyl cellulose). RNA derived from glucose-grown cultures (glu) was compared to RNA derived from polysaccharide-grown cultures (poly) using a dye swap setup.
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Project description:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ⤠0.0001 and |log2 of the ratio of the RPM values| ⥠2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control. After incubation at 45 â, 145rpm for 20 hours with sucrose as the carbon source, mycelia were induced for 16 hours using xylan, cellulose and rice straw, respectively. Transcriptome induced by sucrose was used as the control when comparing the differences between other three transcriptomes (induced by xylan, cellulose and rice straw, respectively).
2015-11-22 | E-GEOD-55086 | biostudies-arrayexpress
Project description:Transcriptional profiling of the A. niger WT (N402) strain treated with xylan (1%, w/v) for 6, 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases after treatment with the polysaccharide xylan. The experiment was further validated by enzymatic assays.
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Project description:Transcriptional profiling of the A. niger WT (N402) strain treated with xylan (1%, w/v) for 6, 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases after treatment with the polysaccharide xylan. The experiment was further validated by enzymatic assays. Three-condition experiment: WT-Xylan for 6, 12 and 24 h at 30oC in batch culture. Firstly, the WT (N402) strain was grown in minimal medium with fructose as carbon source (control), and then transferred to 1% (w/v) xylan as carbon source. 2 biological replicates per time point.
2010-10-21 | E-GEOD-24848 | biostudies-arrayexpress
Project description:CDT-1 and CDT-2 are two cellodextrin transporters discovered in the filamentous fungus Neurospora crassa. Previous studies focused on characterizing the role of these transporters in only a few conditions, including cellulose degradation, and the function of these two transporters is not yet completely understood. In this study, we show that deletion of cdt-2, but not cdt-1, results in growth defects not only on Avicel but also on xylan. cdt-2 can be highly induced by xylan, and this mutant has a xylodextrin consumption defect. Transcriptomic analysis of the cdt-2 deletion strain on Avicel and xylan showed that major cellulase and hemicellulase genes were significantly down-regulated in the cdt-2 deletion strain and artificial over expression of cdt-2 in N. crassa increased cellulase and hemicellulase production. Together, these data clearly show that CDT-2 plays a critical role in hemicellulose sensing and utilization. This is the first time a sugar transporter has been assigned a function in the hemicellulose degradation pathway. Furthermore, we found that the transcription factor XLR-1 is the major regulator of cdt-2, while cdt-1 is primarily regulated by CLR-1. These results deepen our understanding of the functions of both cellodextrin transporters, particularly for CDT-2. Our study also provides novel insight into the mechanisms for hemicellulose sensing and utilization in N. crassa, and may be applicable to other cellulolytic filamentous fungi. N. crassa was pregrown in Sucrose and transferred to Avicel (cellulose) or Xylan(hemicellulose) media. Up regulated and down regulated genes expressions were compared with wild type strain on two conditions (Avicel and xylan) respectively.
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Project description:Herbivorax saccincola A7 is an alkali-thermophilic lignocellulolytic bacterium that was known to possess a strong xylan degradation ability. They can utilize a wide range of carbon sources, however the response and regulation mechanisms to different carbon sources, in terms of genes expression, are still not identified. In this study, H. saccincola A7 was cultured with cellobiose, cellulose, xylan, cellulose-xylan mixture, and empty fruit bunch (EFB) as the sole carbon source. We carried out a comparative expression analysis, focusing on biomass degradation-related genes. The cellulosomal scaffolding proteins and cellulosomal enzymes of H. saccincola A7 were drastically induced when a cellulose-containing substrate was used as a carbon source. On the other hand, xylan induced only some non-cellulosomal enzymes that might be necessary for xylan degradation. The identification of the carbohydrate-sensing mechanism in H. saccincola A7 appeared a similar system as previously described in Clostridium thermocellum. The lignocellulose degradation ability of H. saccincola A7 may be controlled enzyme expression by cellulose-containing substrate, not by xylan. Thus, recognition in the existence of cellulosic substrates is effective in enhancing a high xylan degradation ability in H. saccincola A7.
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Project description:Lignocellulose degradation by microbes plays a central role in global carbon cycling, human gut metabolism, and renewable energy technologies While considerable effort has been put into understanding the biochemical aspects of lignocellulose degradation, much less work has been done to understand how these enzymes work in an in vivo context Here, we report a systems level study of xylan degradation in the saprophytic bacterium Cellvibrio japonicus Transcriptome analysis indicated seven genes that encode carbohydrate active enzymes were up-regulated during growth with xylan containing media In-frame deletion analysis of these genes found that only gly43F is critical for utilization of xylo-oligosaccharides, xylan, and arabinoxylan Heterologous expression of gly43F was sufficient for the utilization of xylo-oligosaccharides in Escherichia coli Additional analysis found that the xyn11A, xyn11B, abf43L, abf43K, and abf51A gene products were critical for utilization of arabinoxylan Furthermore, a predicted transporter (CJA_1315) was required for effective utilization of xylan substrates, and we propose this unannotated gene be called xntA (xylan transporter A) Our major findings are 1) C japonicus employs both secreted and surface associated enzymes for xylan degradation, which differs from the strategy used for cellulose degradation, and 2) a single cytoplasmic β-xylosidase is essential for the utilization of xylo-oligosaccharides
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