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Expression profiling of Cellvibrio japonicus using either glucose, crab shell, or N-acetylglucosamine

ABSTRACT: 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.

ORGANISM(S): Cellvibrio japonicus

PROVIDER: GSE149593 | GEO | 2020/04/30

REPOSITORIES: GEO

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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.

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Expression profiling of Cellvibrio japonicus using either glucose, crab shell, or N-acetylglucosamine

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