Bacterial genomes: what they teach us about cellulose degradation

Brumm, Phillip J.

doi:10.4155/bfs.13.44

Cited by 37 publications

(32 citation statements)

References 83 publications

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“…Genomes of several forest soil bacteria encode proteins involved in decomposition of dead plant biomass (33,(161)(162)(163). In addition to promotion by hydrolytic enzymes, efficient hydrolysis is often promoted by the presence of carbohydrate-binding modules (CBM) that are part of either the enzymes or bacterial cell surfaces (157).…”

Section: Bacterial Involvement In Ecosystem Processes Role Of Bacterimentioning

confidence: 99%

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

Lladó

López-Mondéjar

Baldrián

2017

Microbiol Mol Biol Rev

500

302

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The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.

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Section: Bacterial Involvement In Ecosystem Processes Role Of Bacterimentioning

confidence: 99%

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

Lladó

López-Mondéjar

Baldrián

2017

Microbiol Mol Biol Rev

500

302

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“…Microbial degradation of crystalline cellulose requires the expression and secretion of multiple cellulases and accessory proteins to decrystallize the cellulose chains and generate soluble, low molecular weight cellodextrins (Brumm, 2013). These cellodextrins are then taken up via membrane transporters and further degraded into glucose monomers in the cytoplasm.…”

Section: Resultsmentioning

confidence: 99%

“…All five of the D. turgidum cellulases (Dtur_0276; Dtur_0669; Dtur_0670; Dtur_0671 and Dtur_1586) have orthologs in D. thermophilum (Dicth_0008; Dicth_0505; Dicth_0506; Dicth_0508 and Dicth_1476, respectively). Analysis of the genome shows a lack of GH9, GH6, GH8, GH12, or GH48 cellulases found in truly cellulytic organisms (Brumm, 2013). Close examination of the genome reveals no cellulases containing CBM2 or CBM3 modules present in cellulose-degrading Caldicellulosiruptor species or cellulosomal structures present in cellulose-degrading C. thermocellum species within the genome.…”

Section: Resultsmentioning

confidence: 99%

The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor

et al. 2016

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Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.

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“…Considering that most cellulolytic bacterial CAZymes are often appended to CBMs (Brumm, 2013), it is likely that engineered cellulosomal enzyme complexes could utilize similar mechanisms to generate cello-oligosaccharides for synergistic uptake by CBP bacteria (like C. thermocellum) could allow for more efficient fermentation of cellulosic biomass into ethanol (Lu et al, 2006).…”

Section: Discussionmentioning

confidence: 99%

Carbohydrate binding domains facilitate efficient oligosaccharides synthesis by enhancing mutant catalytic domain transglycosylation activity

Bandi

Gonçalves

Pingali

et al. 2020

Preprint

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Chemoenzymatic approaches using carbohydrate-active enzymes (CAZymes) offer a promising avenue for synthesis of glycans like oligosaccharides. Here, we report a novel chemoenzymatic route for cellodextrins synthesis employed by chimeric CAZymes, akin to native glycosyltransferases, involving the unprecedented participation of a 'noncatalytic' lectin-like or carbohydrate-binding domains (CBMs) in the catalytic step for glycosidic bond synthesis using cellobiosyl donor sugars as activated substrates. CBMs are often thought to play a passive substrate targeting role in enzymatic glycosylation reactions mostly via overcoming substrate diffusion limitations for tethered catalytic domains (CDs) but are not known to participate directly in any nucleophilic substitution mechanisms that impact the actual glycosyl transfer step. Our study provides evidence for the direct participation of CBMs in the catalytic reaction step for -glucan glycosidic bonds synthesis enhancing activity for CBM-based CAZyme chimeras by >140-fold over CDs alone. Dynamic intra-domain interactions that facilitate this poorly understood reaction mechanism were further revealed by small-angle X-ray scattering structural analysis along with detailed mutagenesis studies to shed light on our current limited understanding of similar transglycosylation-type reaction mechanisms. In summary, our study provides a novel strategy for engineering similar CBMbased CAZyme chimeras for synthesis of bespoke oligosaccharides using simple activated sugar monomers. Lombard et al., 2014), and still growing with newly sequenced genomes and metagenomes becoming readily available.CAZymes like GHs or GTs are further classified either as retaining or inverting type, depending on whether the stereochemistry at the anomeric carbon for the product (versus the reactant) is either retained or inverted (Davies and Henrissat, 1995), respectively. As first proposed by Koshland for glycosidases (Koshland, 1953), retaining enzymes require a classical two-step double displacement hydrolysis mechanism (i.e., SN2) with a glycosyl-enzyme intermediate (GEI) formed via a covalent bond between the cleaved substrate and the protein in the alternate orientation (e.g., GEI for retaining enzyme will have an -bond, as opposed to the -orientation of the reactant and product). While most native glycosidases catalyze the hydrolysis of glycosidic linkages, many GHs can also produce oligosaccharides following a competing transglycosylation mechanism if a suitably localized glycosyl acceptor group is present instead of a water molecule within the enzyme active site (Bissaro et al., 2015). Retaining GHs that show significant transglycosylation reactivity are also thought to utilize a similar SN2 type general mechanism, except that rather than nucleophilic attack by water, the attack is instigated by a hydroxyl oxygen on an acceptor sugar placed adjacent to the GEI complex (Figure 1).

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Bacterial genomes: what they teach us about cellulose degradation

Cited by 37 publications

References 83 publications

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor

Carbohydrate binding domains facilitate efficient oligosaccharides synthesis by enhancing mutant catalytic domain transglycosylation activity

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