Growth of Chitinophaga pinensis on Plant Cell Wall Glycans and Characterisation of a Glycoside Hydrolase Family 27 β-l-Arabinopyranosidase Implicated in Arabinogalactan Utilisation

Abstract

The genome of the soil bacterium Chitinophaga pinensis encodes a diverse array of carbohydrate active enzymes, including nearly 200 representatives from over 50 glycoside hydrolase (GH) families, the enzymology of which is essentially unexplored. In light of this genetic potential, we reveal that C. pinensis has a broader saprophytic capacity to thrive on plant cell wall polysaccharides than previously reported, and specifically that secretion of β-l-arabinopyranosidase activity is induced during growth on arabinogalactan. We subsequently correlated this activity with the product of the Cpin_5740 gene, which encodes the sole member of glycoside hydrolase family 27 (GH27) in C. pinensis, CpArap27. Historically, GH27 is most commonly associated with α-d-galactopyranosidase and α-d-N-acetylgalactosaminidase activity. A new phylogenetic analysis of GH27 highlighted the likely importance of several conserved secondary structural features in determining substrate specificity and provides a predictive framework for identifying enzymes with the less common β-l-arabinopyranosidase activity.

Focused Metabolism of β-Glucans by the Soil Bacteroidetes Species Chitinophaga pinensis

“…1b). There was some activity on glucomannan (KGM), but it is perhaps surprising that this was not a more dominant activity, as this is the preferred polysaccharide growth substrate of C. pinensis (13) and is abundant in the wood material. There was also some xylanase activity and some hydrolysis of arabinogalactan.…”

“…The type strain Chitinophaga pinensis is a Bacteroidetes species isolated from softwood forest litter, and it belongs to a genus that is considered to be strongly chitinolytic but not cellulolytic (12). We previously demonstrated the growth of C. pinensis and the induction of specific enzymes by larch wood arabinogalactan (13), and more recently we performed a proteomic assessment comparing enzyme secretion during growth on glucose and complex plant ␤-mannans (14,15). We found that the secretion of a selection of carbohydrate active enzymes (CAZymes) was induced in the presence of ␤-mannan, likely via the action of polysaccharide utilization loci (PULs).…”

“…These are likely to be highly abundant carbon sources in the microhabitat of C. pinensis, where plant matter is bound together in a network-like mat by dead and living mycelium as well as exopolysaccharides secreted by fungi and bacteria. We compare the deconstruction of a range of different ␤-glucans with that of the complex plant heteroglycans glucomannan and arabinoxylan, which contain multiple sugars and linkages and which we have previously shown support growth by C. pinensis (13).…”

Biochemical and structural analyses of a bacterial endo-β-1,2-glucanase reveal a new glycoside hydrolase family

“…C. pinensis is a Gram-negative bacterium that exhibits potential as to the discovery of novel CAZymes (24,40). This bacterium possesses diverse carbohydrate-active enzymes including 191 GHs that can be classified into 56 different families.…”

Draft Genome Sequence of a Chitinophaga Strain Isolated from a Lignocellulose Biomass-Degrading Consortium

“…At the time of writing, the genus Chitinophaga comprises 12 recognized species (4). Brazilian soils with sugarcane culture have many species of the Chitinophagaceae family (4, 5), and an isolate from a bacterial consortium degrading lignocellulose isolated from sugar cane soil was used as study material.…”