Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

Han, Young-Tak; Agarwal, Vinayak; Dodd, Dylan; Kim, Jason; Bae, Byungchan; Mackie, Roderick I.; Nair, Satish K.; Cann, Isaac

doi:10.1074/jbc.m112.391532

Cited by 49 publications

(60 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Bioinformatics analysis of a partial genome sequence of C. polysaccharolyticus revealed two genes that were autoannotated by the RAST server (23)(24)(25) as encoding an ␣-Larabinofuranosidase (CpAbf51A) and an endoarabinanase (CpAbn43A). This observation agreed with the discovery that C. polysaccharolyticus is equipped for the degradation of different polysaccharides (19)(20)(21)26). The genes for polysaccharide degradation in this bacterium are, however, often in a cluster, including the xylan degradation cluster (21) as well as the cluster for mannan degradation (26).…”

Section: Resultssupporting

confidence: 78%

“…CpAbn43A, CpAbf51A, and CpAbf51B were thermostable at high temperatures, retaining 60% of their activity after 24 h at temperatures of up to 70°C. These properties are in agreement with those of other enzymes characterized from C. polysaccharolyticus, including the mannan-degrading enzymes Man5A and Man5B (26) and also the xylan-degrading enzymes from this bacterium (21). CpAbf51B was more stable at 80°C, retaining 75% of its activity after 10 min, while CpAbn43A and CpAbf51A retained only a smaller amount of their activity under the same conditions.…”

Section: Discussionsupporting

confidence: 76%

“…The products of the genes in the putative arabinan degradation cluster were screened for activity with a library of para-nitrophenyl (pNP)-linked sugars as described in our previous publications (21,26). In addition, different plant cell wall polysaccharides were used to evaluate the activities of the enzymes.…”

Section: Resultsmentioning

confidence: 99%

“…This bacterium grows optimally at 65 to 68°C (19), and many of the enzymes characterized from C. polysaccharolyticus have thermostability profiles favorable for biotechnological applications (20)(21)(22).…”

Section: Abstract Pectic Enzymes Thermophilesmentioning

confidence: 99%

See 3 more Smart Citations

Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

Wefers

Dong

Abdelhamid

et al. 2017

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

The plant cell wall polysaccharide arabinan provides an important supply of arabinose, and unraveling arabinan-degrading strategies by microbes is important for understanding its use as a source of energy. Here, we explored the arabinan-degrading enzymes in the thermophilic bacterium Caldanaerobius polysaccharolyticus and identified a gene cluster encoding two glycoside hydrolase (GH) family 51 ␣-L-arabinofuranosidases (CpAbf51A, CpAbf51B), a GH43 endoarabinanase (CpAbn43A), a GH27 ␤-L-arabinopyranosidase (CpAbp27A), and two GH127 ␤-Larabinofuranosidases (CpAbf127A, CpAbf127B). The genes were expressed as recombinant proteins, and the functions of the purified proteins were determined with para-nitrophenyl (pNP)-linked sugars and naturally occurring pectin structural elements as the substrates. The results demonstrated that CpAbn43A is an endoarabinanase while CpAbf51A and CpAbf51B are ␣-L-arabinofuranosidases that exhibit diverse substrate specificities, cleaving ␣-1,2, ␣-1,3, and ␣-1,5 linkages of purified arabinan-oligosaccharides. Furthermore, both CpAbf127A and CpAbf127B cleaved ␤-arabinofuranose residues in complex arabinan side chains, thus providing evidence of the function of this family of enzymes on such polysaccharides. The optimal temperatures of the enzymes ranged between 60°C and 75°C, and CpAbf43A and CpAbf51A worked synergistically to release arabinose from branched and debranched arabinan. Furthermore, the hydrolytic activity on branched arabinan oligosaccharides and degradation of pectic substrates by the endoarabinanase and L-arabinofuranosidases suggested a microbe equipped with diverse activities to degrade complex arabinan in the environment. Based on our functional analyses of the genes in the arabinan degradation cluster and the substrate-binding studies on a component of the cognate transporter system, we propose a model for arabinan degradation and transport by C. polysaccharolyticus. IMPORTANCE Genomic DNA sequencing and bioinformatic analysis allowed the identification of a gene cluster encoding several proteins predicted to function in arabinan degradation and transport in C. polysaccharolyticus. The analysis of the recombinant proteins yielded detailed insights into the putative arabinan metabolism of this thermophilic bacterium. The use of various branched arabinan oligosaccharides provided a detailed understanding of the substrate specificities of the enzymes and allowed assignment of two new GH127 polypeptides as ␤-L-arabinofuranosidases able to degrade pectic substrates, thus expanding our knowledge of this rare group of glycoside hydrolases. In addition, the enzymes showed synergistic effects for the degradation of arabinans at elevated temperatures. The enzymes characterized from the gene cluster are, therefore, of utility for arabinose production in both the biofuel and food industries.

show abstract

Section: Resultssupporting

confidence: 78%

Section: Discussionsupporting

confidence: 76%

Section: Resultsmentioning

confidence: 99%

Section: Abstract Pectic Enzymes Thermophilesmentioning

confidence: 99%

See 2 more Smart Citations

Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

Wefers

Dong

Abdelhamid

et al. 2017

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

show abstract

“…This conclusion was restated in 2002, when the first bacterial FNIII domain tertiary structure was solved, and based on the phylogenetic analysis of 20 of the 135 bacterial FNIII domains, which were at that time (July 2001) listed in SMART [10]. This appears to be the last time that the subject was studied using a bioinformatics analysis, but subsequently it has been referred to in many other FNIII domain studies and reviews (for example [27][28][29][30][31]). The phylogenetic trees presented in this study (Fig.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

The evolutionary origin and possible functional roles of FNIII domains in two Microbacterium aurum B8.A granular starch degrading enzymes, and in other carbohydrate acting enzymes

Valk

Kaaij

Dijkhuizen

2017

Amylase

View full text Add to dashboard Cite

Fibronectin type III (FNIII) domains were first identified in the eukaryotic plasma protein fibronectin, where they act as structural spacers or enable protein-protein interactions. Recently we characterized two large and multi-domain amylases in Microbacterium aurum B8.A that both carry multiple FNIII and carbohydrate binding modules (CBMs). The role of (multiple) FNIII domains in such carbohydrate acting enzymes is currently unclear. Four hypothetical functions are considered here: a substrate surface disruption domain, a carbohydrate binding module, as a stable linker, or enabling protein-protein interactions. We performed a phylogenetic analysis of all FNIII domains identified in proteins listed in the CAZy database. These data clearly show that the FNIII domains in eukaryotic and archaeal CAZy proteins are of bacterial origin and also provides examples of interkingdom gene transfer from Bacteria to Archaea and Eucarya. FNIII domains occur in a wide variety of CAZy enzymes acting on many different substrates, suggesting that they have a non-specific role in these proteins. While CBM domains are mostly found at protein termini, FNIII domains are commonly located between other protein domains. FNIII domains in carbohydrate acting enzymes thus may function mainly as stable linkers to allow optimal positioning and/or flexibility of the catalytic domain and other domains, such as CBM.

show abstract

Production of Cellulolytic Enzymes

Biswas

Persad

Bisaria

2014

Bioprocessing of Renewable Resources to Commodity Bioproducts

View full text Add to dashboard Cite

For the conversion of plant biomass into various bioproducts, a significant bottleneck is enzymatic hydrolysis of lignocelluloses to soluble sugars. These sugars are then metabolized through various natural or engineered pathways toward products of interest. The success of projected biorefinery processes depend to a large extent on the economics of hydrolytic enzyme production. Presently, mesophilic fungal strains

show abstract

Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

Cited by 49 publications

References 61 publications

Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

The evolutionary origin and possible functional roles of FNIII domains in two Microbacterium aurum B8.A granular starch degrading enzymes, and in other carbohydrate acting enzymes

Production of Cellulolytic Enzymes

Contact Info

Product

Resources

About