GH10 XynA is the main xylanase identified in the crude enzymatic extract of Paenibacillus sp. A59 when grown on xylan or lignocellulosic biomass

Production of a bacterial secretome highly efficient for the deconstruction of xylans

Bacteria within the Paenibacillus genus are known to secrete a diverse array of enzymes capable of breaking down plant cell wall polysaccharides. We studied the extracellular xylanolytic activity of Paenibacillus xylanivorans and examined the complete range of secreted proteins when grown on carbohydrate-based carbon sources of increasing complexity, including wheat bran, sugar cane straw, beechwood xylan and sucrose, as control. Our data showed that the relative abundances of secreted proteins varied depending on the carbon source used. Extracellular enzymatic extracts from wheat bran (WB) or sugar cane straw (SCR) cultures had the highest xylanolytic activity, coincidently with the largest representation of carbohydrate active enzymes (CAZymes). Scaling-up to a benchtop bioreactor using WB resulted in a significant enhancement in productivity and in the overall volumetric extracellular xylanase activity, that was further concentrated by freeze-drying. The enzymatic extract was efficient in the deconstruction of xylans from different sources as well as sugar cane straw pretreated by alkali extrusion (SCRe), resulting in xylobiose and xylose, as primary products. The overall yield of xylose released from SCRe was improved by supplementing the enzymatic extract with a recombinant GH43 β-xylosidase (EcXyl43) and a GH62 α-L-arabinofuranosidase (CsAbf62A), two activities that were under-represented. Overall, we showed that the extracellular enzymatic extract from P. xylanivorans, supplemented with specific enzymatic activities, is an effective approach for targeting xylan within lignocellulosic biomass.

Comprehensive Genome Analysis of Cellulose and Xylan-Active CAZymes from the Genus Paenibacillus: Special Emphasis on the Novel Xylanolytic Paenibacillus sp. LS1

Xylan is the most abundant hemicellulose in hardwood and graminaceous plants. It is a heteropolysaccharide comprising different moieties appended to the xylose units. Complete degradation of xylan requires an arsenal of xylanolytic enzymes that can remove the substitutions and mediate internal hydrolysis of the xylan backbone. Here, we describe the xylan degradation potential and underlying enzyme machinery of the strain, Paenibacillus sp. LS1. The strain LS1 was able to utilize both beechwood and corncob xylan as the sole source of carbon, with the former being the preferred substrate. Genome analysis revealed an extensive xylan-active CAZyme repertoire capable of mediating efficient degradation of the complex polymer. In addition to this, a putative xylooligosaccharide ABC transporter and homologues of the enzymes involved in the xylose isomerase pathway were identified. Further, we have validated the expression of selected xylan-active CAZymes, transporters, and metabolic enzymes during growth of the LS1 on xylan substrates using qRT-PCR. The genome comparison and genomic index (average nucleotide identity [ANI] and digital DNA-DNA hybridization) values revealed that strain LS1 is a novel species of the genus Paenibacillus. Lastly, comparative genome analysis of 238 genomes revealed the prevalence of xylan-active CAZymes over cellulose across the Paenibacillus genus. Taken together, our results indicate that Paenibacillus sp. LS1 is an efficient degrader of xylan polymers, with potential implications in the production of biofuels and other beneficial by-products from lignocellulosic biomass. IMPORTANCE Xylan is the most abundant hemicellulose in the lignocellulosic (plant) biomass that requires cooperative deconstruction by an arsenal of different xylanolytic enzymes to produce xylose and xylooligosaccharides. Microbial (particularly, bacterial) candidates that encode such enzymes are an asset to the biorefineries to mediate efficient and eco-friendly deconstruction of xylan to generate products of value. Although xylan degradation by a few Paenibacillus spp. is reported, a complete genus-wide understanding of the said trait is unavailable till date. Through comparative genome analysis, we showed the prevalence of xylan-active CAZymes across Paenibacillus spp., therefore making them an attractive option towards efficient xylan degradation. Additionally, we deciphered the xylan degradation potential of the strain Paenibacillus sp. LS1 through genome analysis, expression profiling, and biochemical studies. The ability of Paenibacillus sp. LS1 to degrade different xylan types obtained from different plant species, emphasizes its potential implication in lignocellulosic biorefineries.

Enzymatic characterization of a novel thermostable and alkaline tolerant GH10 xylanase and activity improvement by multiple rational mutagenesis strategies

Thermo-alkaline xylanases are widely applied in paper pulping industry. In this study, a novel thermostable and alkaline tolerant GH10 xylanase (Xyn30Y5) gene from alkaliphilic Bacillus sp. 30Y5 was cloned and the surface-layer homology (SLH) domains truncated enzyme (Xyn30Y5-SLH) was expressed in Escherichia coli. The purified Xyn30Y5-SLH was most active at 70 °C and pH 7.0 and showed the highest specific activity of 349.4 U mg^-1. It retained more than 90% activity between pH 6.0 to 9.5 and was stable at pH 6.0-10.0. To improve the activity, 47 mutants were designed based on eight rational strategies and 21 mutants showed higher activity. By combinatorial mutagenesis, the best mutant 3B demonstrated specific activity of 1016.8 U mg^-1 with a doubled catalytic efficiency (k_cat/K_m) and RA60_1/2h value, accompanied by optimal pH shift to 8.0. The molecular dynamics simulation analysis indicated that the increase of flexibility of α5 helix and loop7 located near to the catalytic residues is likely responsible for its activity improvement. And the decrease of flexibility of the most unstable regions is vital for the thermostablity improvement. This work provided not only a novel thermostable and alkaline tolerant xylanase with industrial application potential but also an effective mutagenesis strategy for xylanase activity improvement.

Characterization of Aspergillus niger MK981235 xylanase with extraction of anti-hepatotoxic, antioxidant, hypocholesterolemic and prebiotic Corchorus olitorius stems xylooligosaccharides

The object of this study was to utilize agro-industrial waste Corchorus olitorius stems (molokhia stems, MS) as substrate, for Aspergillus niger MK981235 xylanase production and as source of biologically active xylooligosaccharides (XOS). This study succeeded in utilization of Aspergillus niger MK981235 xylanase under different saccharification conditions designed by central composite design (CCD) for extraction of 15 biologically active XOS (anti-hepatotoxic, antioxidant, hypocholesterolemic and prebiotic) with different monosaccharides constituents composition and percent. A. niger MK981235 xylanase showed the highest activity 6.60 U·ml^-1 at 50 °C with 1.5% xylan. The kinetics included K_m and V_max were determined to be 6.67 mg·ml^-1 and 20 μmol·ml^-1·min^-1, respectively. Moreover, A. niger MK981235 xylanase thermodynamics E_a (activation energy) and E_d (activation energy of denaturation) were determined to be 21.95 and 39.51 KJ·mol^-1, respectively. The highest prebiotic effect (growth promation) was exerted by the central MS XOS on Lactobacillus plantarum and Lactobacillus rhamnosus (125 and 135.3%, respectively). Also, the central MS XOS, exerted the highest cholesterol reduction and antioxidant activities 74.7 and 92%, respectively, showed remarkable in vivo protective role against the hepatic toxicity of lithium carbonate evaluated by changes in body weight, liver function markers (AST, ALT, Alb, total bilirubin) and tissue makers (MDA and GSH).

Synergic activity of Cel8Pa β-1,4 endoglucanase and Bg1Pa β-glucosidase from Paenibacillus xylanivorans A59 in beta-glucan conversion

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Cel8Pa is an extracellular, halotolerant, broad substrate endoglucanase.

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Bg1Pa is an intracellular β-glucosidase, with activity on cello oligosaccharides and high resistance to ethanol.

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The concerted action of Cel8Pa and Bg1Pa has a synergistic effect on saccharification of β-glucans.

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Cel8Pa and Bg1Pa are cold-stable and candidates for SSF ethanol 2 G processes.

In the efficient bioconversion of polysaccharides from lignocellulosic biomass, endoglucanases and β-glucosidases are key enzymes for the deconstruction of β-glucans. In this work, we focused on a GH8 endoglucanase (Cel8Pa) and a GH1 β-glucosidase (Bg1Pa) from Paenibacillus xylanivorans A59. Cel8Pa was active on a broad range of substrates, such as β-glucan from barley (24.5 IU/mg), lichenan (17.9 IU/mg), phosphoric acid swollen cellulose (PASC) (9.7 IU/mg), carboxi-methylcellulose (CMC) (7.3 IU/mg), chitosan (1.4 IU/mg) and xylan (0.4 IU/mg). Bg1Pa was active on cellobiose (C2) and cello-oligosaccharides up to C6, releasing glucose as the main product. When both enzymes were used jointly, there was a synergic effect in the conversion rate of polysaccharides to glucose. Cel8Pa and Bg1Pa presented important properties for simultaneous saccharification and fermentation (SSF) processes in second generation bioethanol production, such as tolerance to high concentration of glucose and ethanol.

Paenibacillus xylanivorans sp. nov., a xylan-degrading bacterium isolated from decaying forest soil

A xylanolytic bacterial strain, named A59^T, was isolated from a forest soil consortium in southern Argentina. Strain A59^T is a Gram-stain-positive, facultative anaerobic, endospore-forming and rod-shaped bacterium. Its optimal growth conditions are 30 °C (range, 28-37 °C), pH 7 (range, pH 5-10) and it tolerates up to 7 % of NaCl (range, 2-7 %). Chemotaxonomic analysis revealed that strain A59^Tpossesses meso-diaminopimelic acid in the cell wall. It contains menaquinone MK-7 as the predominant isoprenoid quinone and the major fatty acid is anteiso-C_15 : 0 (35.1 %), with a moderate amount of C_16 : 0 (6.9 %). According to 16S RNA gene sequence analysis, the isolate is phylogenetically placed in the same cluster as Paenibacillus taichungensis BCRC 17757^T (99.7 % nucleotide sequence identity) and Paenibacillus pabuli NBRC 13638^T (99.1 %) and is closely related to Paenibacillus tundrae A10b^T (98.8 %). However, phylogenetic studies based on the housekeeping gyrB gene placed A59^T in a separate branch from all other related type strains. Furthermore, the results of whole genome average nucleotide identity analysis (gANI) with related type strains was lower than 91.10 % and the digital DNA-DNA hybridization value was lower than 44.30 %, which are below the threshold values for separating two species. The DNA G+C content was estimated as 46.09 mol%, based on genome sequencing. On the basis of these results, A59^T represents a new species of the genus Paenibacillus, and we propose the name Paenibacillusxylanivorans sp. nov. The type strain is A59^T (=DSM 107920^T=NCIMB 15123^T).

Endoglucanase improve the growth of homofermentative Lactobacillus spp. in ensilages

Endoglucanase, an important component of cellulases, is used as additives in ensiling of forage crops. However, its detailed role is unclear in ensilages. In the present study, two endoglucanases Cel5 and Cel9 produced by strain Paenibacillus panacisoli SDMCC050309, previously isolated from ensiled corn stover, were identified in the cultures by microcrystalline cellulose absorption coupled with zymogram analysis. After heterologously expressed in Escherichia coli DE3 and purified, these two proteins were biochemically characterized. Cel5 was 61 kDa and showed maximal activity at pH 7.0 and 45 °C, while the maximum activity was at pH 8.0 and 65 °C for Cel9 with 97 kDa in size. Both of them could degrade carboxymethyl cellulose into cellooligosaccharides, in which cellobiose and cellotriose could be used as substrates for the growth of homofermentative strains Lactobacillus plantarum CGMCC6888 and L. farciminis CCTCC AB2016237, but not for the heterofermentative strains L. brevis SDMCC050297 and L. parafarraginis SDMCC050300. Therefore, we concluded that the added endoglucanase contributed to enhance the growth of homofermentative lactic acid bacteria for high level of lactic acid production in ensilages.

Mining the biomass deconstructing capabilities of rice yellow stem borer symbionts

BACKGROUND

Efficient deconstruction of lignocellulosic biomass into simple sugars in an economically viable manner is a prerequisite for its global acceptance as a feedstock in bioethanol production. This is achieved in nature by suites of enzymes with the capability of efficiently depolymerizing all the components of lignocellulose. Here, we provide detailed insight into the repertoire of enzymes produced by microorganisms enriched from the gut of the crop pathogen rice yellow stem borer (Scirpophaga incertulas).

RESULTS

A microbial community was enriched from the gut of the rice yellow stem borer for enhanced rice straw degradation by sub-culturing every 10 days, for 1 year, in minimal medium with rice straw as the main carbon source. The enriched culture demonstrated high cellulolytic and xylanolytic activity in the culture supernatant. Metatranscriptomic and metaexoproteomic analysis revealed a large array of enzymes potentially involved in rice straw deconstruction. The consortium was found to encode genes ascribed to all five classes of carbohydrate-active enzymes (GHs, GTs, CEs, PLs, and AAs), including carbohydrate-binding modules (CBMs), categorized in the carbohydrate-active enzymes (CAZy) database. The GHs were the most abundant class of CAZymes. Predicted enzymes from these CAZy classes have the potential to digest each cell-wall components of rice straw, i.e., cellulose, hemicellulose, pectin, callose, and lignin. Several identified CAZy proteins appeared novel, having an unknown or hypothetical catalytic counterpart with a known class of CBM. To validate the findings, one of the identified enzymes that belong to the GH10 family was functionally characterized. The enzyme expressed in E. coli efficiently hydrolyzed beechwood xylan, and pretreated and untreated rice straw.

CONCLUSIONS

This is the first report describing the enrichment of lignocellulose degrading bacteria from the gut of the rice yellow stem borer to deconstruct rice straw, identifying a plethora of enzymes secreted by the microbial community when growing on rice straw as a carbon source. These enzymes could be important candidates for biorefineries to overcome the current bottlenecks in biomass processing.

Increase in the Production of Endo-1,4-β-Xylanase from Paenibacillus brasilensis in Pichia pastoris

A Pichia pastoris yeast strain producing endo-l,4-β-xylanase from Paenibacillus brasilensis with an activity of 54,400 U/mL after 140 h of fermentation in a laboratory fermenter has been obtained. A number of approaches were used to increase the level of the xylanase production in this strain: optimization of the target gene codon composition, multiple integration of the expression cassette into the recipient strain chromosome using the Cre-lox recombination system, and also improving the heterologous protein folding via the overexpression of the HAC1i gene from Pichia pastoris. xylanase, xylan, Cre-lox system, HAC1p transcriptional activator, multicopy strain, Paenibacillus brasilensis, Pichia pastoris The work was performed with the financial support of the Ministry of Education and Science of Russia (Unique Project Identifier RFMEFI60717X0180) using the Multipurpose Scientific Installation of «All-Russian Collection of Industrial Microorganisms» National Bio-Resource Center, NRC «Kurchatov Institute» - GosNIIgenetika.

Genomically Defined Paenibacillus polymyxa ND24 for Efficient Cellulase Production Utilizing Sugarcane Bagasse as a Substrate

Cellulolytic bacteria from cattle rumen with ability to hydrolyze cellulose rich biomass were explored. The study selected Paenibacillus polymyxa ND24 from 847 isolates as the most potent strain, which can efficiently produce cellulase by utilizing sugarcane bagasse, rice straw, corn starch, CMC, and avicel as a sole carbon source. On annotation of P. polymyxa ND24 genome, 116 members of glycoside hydrolase (GH) family from CAZy clusters were identified and the presence of 10 potential cellulases was validated using protein folding information. Cellulase production was further demonstrated at lab-scale 5-L bioreactor exhibiting maximum endoglucanase activity up to 0.72 U/mL when cultivated in the medium containing bagasse (2% w/v) after 72 h. The bagasse hydrolysate so produced was further utilized for efficient biogas production. The presence of diverse hydrolytic enzymes and formidable cellulase activity supports the use of P. polymyxa ND24 for cost-effective bioprocessing of cellulosic biomass.

Paenibacillus panacisoli enhances growth of Lactobacillus spp. by producing xylooligosaccharides in corn stover ensilages

The knowledge about the association of lignocellulosic biomass-degrading microbes with lactic acid bacteria (LAB) in ensilages is still limited. Paenibacillus strains are important microbes in sustainable agriculture. Here, P. panacisoli SDMCC050309 was isolated from ensiled corn stover and used as an example to investigate the effects on LAB. This strain produced at least 7 xylanases, and two of them were purified and characterized. Temperature and pH optima were determined to be 55 °C and 8.0 for Xyn10 and 40 °C and 7.0 for Xyn11, respectively. They could degraded larch wood xylan and alkali-pretreated corn stover into xylooligosaccharides (XOS). Using the produced XOS to culture Lactobacillus brevis SDMCC050297 and L. parafarraginis SDMCC050300, both of them grew well with high level of acetic acid production. The same phenomenon was observed when co-culturing those two Lactobacillus strains with P. panacisoli SDMCC050309. Therefore, P. panacisoli enhances growth of LAB by producing XOS in corn stover ensilages.