Analysis of the Structural and Functional Diversity of Plant Cell Wall Specific Family 6 Carbohydrate Binding Modules

Biochemistry ◽  
2009 ◽  
Vol 48 (43) ◽  
pp. 10395-10404 ◽  
Author(s):  
D. Wade Abbott ◽  
Elizabeth Ficko-Blean ◽  
Alicia Lammerts van Bueren ◽  
Artur Rogowski ◽  
Alan Cartmell ◽  
...  
Keyword(s):  
Cell Wall ◽  
Functional Diversity ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

Glycoside hydrolase carbohydrate-binding modules as molecular probes for the analysis of plant cell wall polymers

2004 ◽  
Vol 326 (1) ◽  
pp. 49-54 ◽  
Author(s):  
Lesley McCartney ◽  
Harry J Gilbert ◽  
David N Bolam ◽  
Alisdair B Boraston ◽  
J.Paul Knox
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Glycoside Hydrolase ◽  
Plant Cell Wall ◽  
Molecular Probes ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
Cell Wall Polymers

scholarly journals Crystallization and preliminary crystallographic studies of a novel noncatalytic carbohydrate-binding module from theRuminococcus flavefacienscellulosome

2015 ◽  
Vol 71 (1) ◽  
pp. 45-48 ◽  
Author(s):  
Immacolata Venditto ◽  
Arun Goyal ◽  
Andrew Thompson ◽  
Luis M. A. Ferreira ◽  
Carlos M. G. A. Fontes ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Cellulolytic Bacterium ◽  
Modular Architecture ◽  
Carbohydrate Binding Modules ◽  
Fundamental Biological Process

Microbial degradation of the plant cell wall is a fundamental biological process with considerable industrial importance. Hydrolysis of recalcitrant polysaccharides is orchestrated by a large repertoire of carbohydrate-active enzymes that display a modular architecture in which a catalytic domain is connectedvialinker sequences to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs direct the appended catalytic modules to their target substrates, thus potentiating catalysis. The genome of the most abundant ruminal cellulolytic bacterium,Ruminococcus flavefaciensstrain FD-1, provides an opportunity to discover novel cellulosomal proteins involved in plant cell-wall deconstruction. It encodes a modular protein comprising a glycoside hydrolase family 9 catalytic module (GH9) linked to two unclassified tandemly repeated CBMs (termed CBM-Rf6A and CBM-Rf6B) and a C-terminal dockerin. The novel CBM-Rf6A from this protein has been crystallized and data were processed for the native and a selenomethionine derivative to 1.75 and 1.5 Å resolution, respectively. The crystals belonged to orthorhombic and cubic space groups, respectively. The structure was solved by a single-wavelength anomalous dispersion experiment using theCCP4 program suite andSHELXC/D/E.

scholarly journals Insights into Plant Cell Wall Degradation from the Genome Sequence of the Soil Bacterium Cellvibrio japonicus

2008 ◽  
Vol 190 (15) ◽  
pp. 5455-5463 ◽  
Author(s):  
Robert T. DeBoy ◽  
Emmanuel F. Mongodin ◽  
Derrick E. Fouts ◽  
Louise E. Tailford ◽  
Hoda Khouri ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Soil Bacterium ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
Cellvibrio Japonicus ◽  
And Storage

ABSTRACT The plant cell wall, which consists of a highly complex array of interconnecting polysaccharides, is the most abundant source of organic carbon in the biosphere. Microorganisms that degrade the plant cell wall synthesize an extensive portfolio of hydrolytic enzymes that display highly complex molecular architectures. To unravel the intricate repertoire of plant cell wall-degrading enzymes synthesized by the saprophytic soil bacterium Cellvibrio japonicus, we sequenced and analyzed its genome, which predicts that the bacterium contains the complete repertoire of enzymes required to degrade plant cell wall and storage polysaccharides. Approximately one-third of these putative proteins (57) are predicted to contain carbohydrate binding modules derived from 13 of the 49 known families. Sequence analysis reveals approximately 130 predicted glycoside hydrolases that target the major structural and storage plant polysaccharides. In common with that of the colonic prokaryote Bacteroides thetaiotaomicron, the genome of C. japonicus is predicted to encode a large number of GH43 enzymes, suggesting that the extensive arabinose decorations appended to pectins and xylans may represent a major nutrient source, not just for intestinal bacteria but also for microorganisms that occupy terrestrial ecosystems. The results presented here predict that C. japonicus possesses an extensive range of glycoside hydrolases, lyases, and esterases. Most importantly, the genome of C. japonicus is remarkably similar to that of the gram-negative marine bacterium, Saccharophagus degradans 2-40T. Approximately 50% of the predicted C. japonicus plant-degradative apparatus appears to be shared with S. degradans, consistent with the utilization of plant-derived complex carbohydrates as a major substrate by both organisms.

scholarly journals Proteomic Characterization of Lignocellulolytic Enzymes Secreted by the Insect-Associated Fungus Daldinia decipiens oita, Isolated from a Forest in Northern Japan

2020 ◽  
Vol 86 (8) ◽  
Author(s):  
Chiaki Hori ◽  
Ruopu Song ◽  
Kazuki Matsumoto ◽  
Ruy Matsumoto ◽  
Benjamin B. Minkoff ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Glycoside Hydrolases ◽  
Wall Material ◽  
Carbohydrate Binding ◽  
Symbiotic Fungus ◽  
Proteomic Approach ◽  
Carbohydrate Binding Modules ◽  
Activity Measurements

ABSTRACT Wood-devastating insects utilize their symbiotic microbes with lignocellulose-degrading abilities to extract energy from recalcitrant woods. It is well known that free-living lignocellulose-degrading fungi secrete various carbohydrate-active enzymes (CAZymes) to degrade plant cell wall components, mainly cellulose, hemicellulose, and lignin. However, CAZymes from insect-symbiotic fungi have not been well documented except for a few examples. In this study, an insect-associated fungus, Daldinia decipiens oita, was isolated as a potential symbiotic fungus of female Xiphydria albopicta captured from Hokkaido forest. This fungus was grown in seven different media containing a single carbon source, glucose, cellulose, xylan, mannan, pectin, poplar, or larch, and the secreted proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 128 CAZymes, including domains of 92 glycoside hydrolases, 15 carbohydrate esterases, 5 polysaccharide lyases, 17 auxiliary activities, and 11 carbohydrate-binding modules, were identified, and these are involved in degradation of cellulose and hemicellulose but not lignin. Together with the results of polysaccharide-degrading activity measurements, we concluded that D. decipiens oita tightly regulates the expression of these CAZymes in response to the tested plant cell wall materials. Overall, this study described the detailed proteomic approach of a woodwasp-associated fungus and revealed that the new isolate, D. decipiens oita, secretes diverse CAZymes to efficiently degrade lignocellulose in the symbiotic environment. IMPORTANCE Recent studies show the potential impacts of insect symbiont microbes on biofuel application with regard to their degradation capability of a recalcitrant plant cell wall. In this study, we describe a novel fungal isolate, D. decipiens oita, as a single symbiotic fungus from the Xiphydria woodwasp found in the northern forests of Japan. Our detailed secretome analyses of D. decipiens oita, together with activity measurements, reveal that this insect-associated fungus exhibits high and broad activities for plant cell wall material degradation, suggesting potential applications within the biomass conversion industry for plant mass degradation.

scholarly journals Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

2014 ◽  
Vol 81 (4) ◽  
pp. 1375-1386 ◽  
Author(s):  
Xin Dai ◽  
Yan Tian ◽  
Jinting Li ◽  
Xiaoyun Su ◽  
Xuewei Wang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Average Length ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Cell Wall Polysaccharide ◽  
Cell Wall Polysaccharides ◽  
Content Type ◽  
Carbohydrate Binding Modules

ABSTRACTThe bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for ∼1% and ∼0.1% of the total non-rRNAs, respectively. The majority (∼98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized byRuminococcusandFibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the generaRuminococcus,Prevotella, andFibrobacter. Most (∼82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the generaRuminococcus,Fibrobacter, andPrevotellaare predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen.

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