Genome analyses highlight the different biological roles of cellulases

Medie, Felix Mba; Davies, G.J.; Drancourt, Michel; Henrissat, Bernard

doi:10.1038/nrmicro2729

Cited by 187 publications

(153 citation statements)

References 47 publications

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“…Thus, our data likely represent a lower bound of the distribution of the considered GH families in nature. It is also important to recognize that not all glycoside hydrolase genes analyzed here encode proteins involved in the degradation of cellulose or oligosaccharides (15). Based on our analysis, at least 75% of the cellulases from GH8 are involved in the cellulose production in Proteobacteria.…”

Section: Figmentioning

confidence: 88%

“…The biochemistry (the catalytic mechanisms, the kinetics, the substrate binding) of many GH is well characterized (1,(15)(16)(17)(18). This information, together with comparisons of some structures and sequences, resulted in an accurate GH classification (9,19,20).…”

mentioning

confidence: 99%

“…This information, together with comparisons of some structures and sequences, resulted in an accurate GH classification (9,19,20). Moreover, a few cellulolytic strains have also been subjected to thorough characterization and to sequencing of their genomes (1,15). Recently, GH-specific annotation systems were introduced in order to precisely assign function to newly sequenced GH (21,22).…”

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confidence: 99%

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Phylogenetic Distribution of Potential Cellulases in Bacteria

Berlemont

Martiny

2013

Appl Environ Microbiol

256

233

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Many microorganisms contain cellulases that are important for plant cell wall degradation and overall soil ecosystem functioning. At present, we have extensive biochemical knowledge of cellulases but little is known about the phylogenetic distribution of these enzymes. To address this, we analyzed the distribution of 21,985 genes encoding proteins related to cellulose utilization in 5,123 sequenced bacterial genomes. First, we identified the distribution of glycoside hydrolases involved in cellulose utilization and synthesis at different taxonomic levels, from the phylum to the strain. Cellulose degradation/utilization capabilities appeared in nearly all major groups and resulted in strains displaying various enzyme gene combinations. Potential cellulose degraders, having both cellulases and ␤-glucosidases, constituted 24% of all genomes whereas potential opportunistic strains, having ␤-glucosidases only, accounted for 56%. Finally, 20% of the bacteria have no relevant enzymes and do not rely on cellulose utilization. The latter group was primarily connected to specific bacterial lifestyles like autotrophy and parasitism. Cellulose degraders, as well as opportunists, have multiple enzymes with similar functions. However, the potential degraders systematically harbor about twice more ␤-glucosidases than their potential opportunistic relatives. Although scattered, the distribution of functional types, in bacterial lineages, is not random but mostly follows a Brownian motion evolution model. Degraders form clusters of relatives at the species level, whereas opportunists are clustered at the genus level. This information can form a mechanistic basis for the linking of changes in microbial community composition to soil ecosystem processes.

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Section: Figmentioning

confidence: 88%

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confidence: 99%

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confidence: 99%

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Phylogenetic Distribution of Potential Cellulases in Bacteria

Berlemont

Martiny

2013

Appl Environ Microbiol

256

233

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“…Complete enzymatic hydrolysis and breakdown of cellulose chains require the combined activities of the β-1,4-glycosidic bond-cleaving enzymes endoglucanase (EG), cellobiohydrolase (CBH), and β-glucosidase (BGL). β-1,4-endoglucanases hydrolyze the non-crystalline regions of cellulose microfibrils, while CBH enzymes digest the ends of cellulose chains (Medie et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Profile of Lignocellulose Degradation from Trametes versicolor on Poplar Wood

Zhang

Wang

et al. 2017

BioResources

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The Trametes versicolor genome is predicted to encode many enzymes that effectively degrade lignin, making it a potentially useful tool for biopulping. However, the wood degradation mechanism of T. versicolor is not clear. To identify the enzymes that contribute to lignocellulose degradation, changes in the T. versicolor transcriptome during growth on poplar wood, relative to growth on glucose medium, were evaluated. Eight hundred and fifty-three genes were differentially expressed, with 360 genes up-regulated and 493 genes were down-regulated on poplar wood. Notably, most genes involved in lignin degradation were upregulated, including eight lignin peroxidase (LiP) genes. Genes encoding cellulose and hemicellulose degrading-enzymes were mostly downregulated, including six endo-β-1,4-glucanase genes and three cellobiohydrolase I genes. These results characterized transcriptomic changes related to lignocellulose degradation. This information could be used to develop T. versicolor as a tool to improve the efficiency of lignin degradation or to provide a theoretical foundation for a new paper pulp manufacturing process.

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“…Niektóre geny celulaz, składowe operonu odpowiedzialnego za syntezę celulozy, są zaangażowane w biosyntezę tego cukru, jakkolwiek wśród mikrobiontów jelitowych u kurcząt nie stwierdza się ich zaangażowania w syntezę celulozy (56). Niektórzy przedstawiciele Clostridiales mają geny endonukleaz odpowiedzialnych za sporulacje.…”

Section: Znaczenie Mikrobiomu Jelitowegounclassified

Chicken intestinal microbiome: Development and function

Binek¹,

Cisek²,

Rzewuska³

et al. 2017

Medycyna Weterynaryjna

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SummaryChicken ceca contain an immense number of microorganisms collectively known as the microbiome. This community is now recognized as an essential component of the intestinal ecosystem and referred to as a metabolic organ exquisitely tuned to the host's physiology. These functions include the ability to process otherwise indigestible components of the feed, converting them into energy and body mass. The gut microbiome can also affect intestinal morphology and modulate the development and function of the immune system. This microbiota contains a rich collection of genes encoding enzymes necessary for decomposition of dietary polysaccharides and oligosaccharides, nitrogen metabolism, fatty acid and lipid metabolism, and pathways involved in a hydrogen sink. Chickens, like most animals, lack the genes for glycoside hydrolase, polysaccharide lyase, and carbohydrate esterase enzymes that are necessary to facilitate the degradation of non-starch polysaccharides. During the decomposition of dietary polysaccharides, bacteria produce short-chain (volatile) fatty acids (SCFAs), such as acetic, propionic and butyric acid. These SCFASs are absorbed transepithelially and serve as a source of energy for the host. The accumulation of molecular hydrogen released during fermentation leads to fermentation slowdown or to the production of less energy-efficient substances, such as ethanol, butyrate and propionate. The presence of bacteria that act as a hydrogen sink results in a switch to the more productive fermentation into acetate and increased production of SCFAs. Such activity could lead to a significant improvement in poultry production and the associated economics.

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Genome analyses highlight the different biological roles of cellulases

Cited by 187 publications

References 47 publications

Phylogenetic Distribution of Potential Cellulases in Bacteria

Phylogenetic Distribution of Potential Cellulases in Bacteria

Transcriptomic Profile of Lignocellulose Degradation from Trametes versicolor on Poplar Wood

Chicken intestinal microbiome: Development and function

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