Ontology highlight
ABSTRACT:
PROVIDER: PRJNA561085 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR9997330_1.fastq.gz | Fastqsanger.gz | |||
| SRR9997330_2.fastq.gz | Fastqsanger.gz | |||
| SRR9997331_1.fastq.gz | Fastqsanger.gz | |||
| SRR9997331_2.fastq.gz | Fastqsanger.gz |
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Project description:Investigation of whole genome gene expression level changes in Cellvibrio japonicus wild-type, comparing glucose vs cellulose. Study was purposed with determining changes in polysaccharide degradation pathways during utilization of insoluble cellulose.
2014-10-07 | GSE62106 | GEO
Project description:Study of the secretome of Cellvibrio japonicus after growth on different chitins. Utilization of a novel plate method to enrich truly secreted proteins.
2016-05-18 | PXD002843 | Pride
Project description:Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes, many of which have been categorized as functionally redundant. Here we present data that suggests that carbohydrate active enzymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted b-glucosidases is required in a physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual b-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Our approach for parsing related carbohydrate active enzymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.
2017-01-01 | GSE90955 | GEO
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
2018-01-15 | GSE108095 | GEO
Project description:Microbial deconstruction of plant polysaccharides is important for environmental nutrient cycling, and bacteria proficient at this process have extensive suites of polysaccharide-specific enzymes. In the Gram-negative saprophyte Cellvibrio japonicus, genome annotation suggests that 17 genes are predicted to encode Carbohydrate-Active enZymes (CAZymes) with roles in cellulose degradation, however previous work suggested that only a subset of these genes is essential. Building upon that work, here we identify the required and minimally sufficient set of enzymes for complete degradation of cellulose using a combination of transcriptomics, gene deletion analysis, heterologous expression studies, and metabolite analysis. We identified six CAZyme-encoding required for cellulose deconstruction in C. japonicus, which are cel3B, cel5B, cel6A, lpmo10B, cbp2D, and cbp2E. These genes encode for a β-glucosidase, an endoglucanase, a cellbiohydrolase, a lytic polysaccharide mono-oxygenase, and two carbohydrate-binding proteins, respectively. These CAZyme-encoding genes are essential for growth using insoluble cellulose by C. japonicus, and sufficient using soluble cellulose when heterologously expressed in Escherichia coli. Moreover, during C. japonicus grow using insoluble cellulose we detected no cellodextrins in the medium, which suggests that cello-oligosaccharide uptake is highly efficient. RNAseq analysis corroborates these results, as we observed several genes significantly up-regulated during growth on cellulose that encode TonB-dependent and ABC transporters. Our revised model of cellulose utilization by C. japonicus suggests a greater importance for the Cbp2D and Cbp2E proteins than previously thought and that rapid cellodextrin update by C. japonicus is a mechanism to maximize the energetic return on investment for the production and secretion of CAZymes.
2025-01-21 | GSE287208 | GEO
Project description:Chitin utilization by microbes plays a significant role in cycling of carbon and nitrogen in the biosphere, and the study of the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade this recalcitrant polysaccharide. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and non-redundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics, bacterial genetics, and complex environmental substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in Cellvibrio japonicus. Using RNAseq analysis we found not only the up-regulation of genes that encode CAZymes specific for chitin metabolism but also a coordinated expression of non-chitin specific CAZyme genes. Furthermore, we used mutational analysis to characterize the hex20B gene product, predicted to encode a hexosaminidase, and found that it is required for efficient utilization of chito-oligosaccharides. Surprisingly, two additional gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were essential for shuttling chito-oligosaccharides into the periplasmic space. Here we propose naming these loci cttA (chito-oligosaccharides transporter A) and cttB respectively. This study further develops our model of how C. japonicus can derive nutrients from recalcitrant chitin-containing substrates and may be potentially useful for other environmentally or industrially important bacteria.
2020-04-30 | GSE149593 | GEO
Project description:Plant mannans are a component of lignocellulose that may possess diverse compositions changing both in terms of its backbone and side-chain substitutions. Consequently, the degradation of mannan substrates requires a cadre of enzymes for complete reduction to substituent monosaccharides, specifically mannose, galactose, and/or glucose. One bacterium that possesses this suite of enzymes is the Gram-negative saprophyte Cellvibrio japonicus, which has ten predicted mannanases from the Glycoside Hydrolase (GH) families 5, 26, and 27. Here we describe a systems biology approach to identify and characterize the essential components of the mannan degradation apparatus in this bacterium. Transcriptomic analysis uncovered significant changes in gene expression for most mannanases, as well as many genes that encode Carbohydrate Active Enzymes (CAZymes) when mannan substrates were actively being degraded. A comprehensive mutational analysis characterized 54 CAZyme genes in the context of mannan utilization. Growth analysis of the mutant strains indicated that the man26C, aga27A, and man5D genes, which encode a mannobiohydrolase, α- galactosidase, and mannosidase, respectively, were influential to the deconstruction of galactomannan. Furthermore, our updated model of mannan degradation in C. japonicus proposes that the removal of galactose sidechains from substituted mannans constitutes a crucial step for the efficient and complete degradation of this hemicellulose by bacteria.
2022-06-28 | GSE206864 | GEO
Project description:Understanding the strategies used by bacteria to degrade polysaccharides constitutes an invaluable tool for biotechnological applications Bacteria are major mediators of polysaccharide degradation in nature, however the complex mechanisms used to detect, degrade, and consume these substrates are not well understood, especially for recalcitrant polysaccharides such as chitin It has been previously shown that the model bacterial saprophyte Cellvibrio japonicus is able to catabolize chitin, but little is known about the enzymatic machinery underlying this capability Previous analyses of the C japonicus genome and proteome indicated the presence of four family 18 Glycoside Hydrolase (GH18) enzymes, and studies of the proteome indicated that all are involved in chitin utilization Using a combination of in vitro and in vivo approaches, we have studied the roles of these four chitinases in chitin bioconversion Genetic analyses showed that only the chi18D gene product is essential for the degradation of chitin substrates Biochemical characterization of the four enzymes showed functional differences and synergistic effects during chitin degradation, indicating non-redundant roles in the cell Transcriptomic studies revealed complex regulation of the chitin degradation machinery of C japonicus and confirmed the importance of CjChi18D and CjLPMO10A, a previously characterized chitin-active enzyme With this systems biology approach, we deciphered the physiological relevance of the GH18 enzymes for chitin degradation in C japonicus, and the combination of in vitro and in vivo approaches provided a comprehensive understanding of the initial stages of chitin degradation by this bacterium
2018-01-24 | GSE108935 | GEO
Project description:Background: Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to an innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo-xyloglucanases were unresolved. Results: Combined bioinformatic and transcriptomic analyses implicated three Glycoside Hydrolase Family 5 Subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone endo-xyloglucanases in C. japonicus. Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose. Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known exo-glycosidases. Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes. Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in C. japonicus. Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the endo-xyloglucanases characterized here. Conclusions: Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of C. japonicus. The detailed structural-functional characterization of three distinct GH5_4 endo-xyloglucanases will inform future bioinformatics predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications.
2018-01-25 | GSE109594 | GEO