Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199

Abstract

BackgroundThe search for new enzymes and microbial strains to degrade plant biomass is one of the most important strategies for improving the conversion processes in the production of environment-friendly chemicals and biofuels. In this study, we report a new Paenibacillus isolate, O199, which showed the highest efficiency for cellulose deconstruction in a screen of environmental isolates. Here, we provide a detailed description of the complex multi-component O199 enzymatic system involved in the degradation of lignocellulose.ResultsWe examined the genome and the proteome of O199 grown on complex lignocellulose (wheat straw) and on microcrystalline cellulose. The genome contained 476 genes with domains assigned to carbohydrate-active enzyme (CAZyme) families, including 100 genes coding for glycosyl hydrolases (GHs) putatively involved in cellulose and hemicellulose degradation. Moreover, 31 % of these CAZymes were expressed on cellulose and 29 % on wheat straw. Proteomic analyses also revealed a complex and complete set of enzymes for deconstruction of cellulose (at least 22 proteins, including 4 endocellulases, 2 exocellulases, 2 cellobiohydrolases and 2 β-glucosidases) and hemicellulose (at least 28 proteins, including 5 endoxylanases, 1 β-xylosidase, 2 xyloglucanases, 2 endomannanases, 2 licheninases and 1 endo-β-1,3(4)-glucanase). Most of these proteins were secreted extracellularly and had numerous carbohydrate-binding domains (CBMs). In addition, O199 also secreted a high number of substrate-binding proteins (SBPs), including at least 42 proteins binding carbohydrates. Interestingly, both plant lignocellulose and crystalline cellulose triggered the production of a wide array of hydrolytic proteins, including cellulases, hemicellulases, and other GHs.ConclusionsOur data provide an in-depth analysis of the complex and complete set of enzymes and accessory non-catalytic proteins—GHs, CBMs, transporters, and SBPs—implicated in the high cellulolytic capacity shown by this bacterial strain. The large diversity of hydrolytic enzymes and the extracellular secretion of most of them supports the use of Paenibacillus O199 as a candidate for second-generation technologies using paper or lignocellulosic agricultural wastes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0518-x) contains supplementary material, which is available to authorized users.

Agrowastes as Feedstock for the Production of Endo-β-Xylanase from <b><i>Cohnella</i></b> sp. Strain AR92

“…NZ_AZXQ00000000.1]. Cells growing attached to the debris of lignocellulosic substrates were reported for members of the Paenibacillaceae family, with extracellular surface layer-associated GHs [López-Mondéjar et al, 2016;Pason et al, 2006;St John et al, 2012]. In agreement, the cells of the strain AR92 were observed growing attached to insoluble OH-SCB, frequently imbibed into amorphous structures ( Fig.…”

“…Numerous reports have highlighted the extensive and unexplored diversity of the prokaryotic enzymatic systems involved, thereby contributing to unravelling the role of bacterial taxa in the decomposition of plant polysaccharides [Berlemont and Martiny, 2013;López-Mondéjar et al, 2016].…”

Isolation and characterization ofRhizobiumsp. strain YS-1r that degrades lignin in plant biomass

“…; Lopez‐Mondejar et al . ). These in silico observations are corroborated by the observed growth of strain Y‐1r (increased from 10 3 –10 8 CFU per ml in 2 weeks) in microcosms containing crystalline cellulose, cellobiose or xylan as the sole carbon source (data not shown).…”

“…Similarly, several genes that code for enzymes implicated in the degradation of hemicellulose were detected in the genome. For example, genes for alpha-arabinofuranosidase, beta-galactosidase/beta-glucuronidase, beta-mannosidas, beta-xylosidase and several GH families (GH 2, GH 16, GH 28, GH 31, GH 42 and GH 43) necessary for hemicellulose degradation were found in the genome (Lombard et al 2014;Lopez-Mondejar et al 2016). These in silico observations are corroborated by the observed growth of strain Y-1r (increased from 10 3 -10 8 CFU per ml in 2 weeks) in microcosms containing crystalline cellulose, cellobiose or xylan as the sole carbon source (data not shown).…”

Genome Structure ofBacillus cereustsu1 and Genes Involved in Cellulose Degradation and Poly-3-Hydroxybutyrate Synthesis

“…T [33][34][35] was obtained from the Bacillus Genetic Stock Center (Columbus, OH). In these assays, P. polymyxa 25A2…”