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Genomic analysis of Paenibacillus macerans strain I6, which can effectively saccharify oil palm empty fruit bunches under nutrient-free conditions
(2023-07-01)
Uke, Ayaka
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Sornyotha, Somphit
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Baramee, Sirilak
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Tachaapaikoon, Chakrit
;
Pason, Patthra
The improper disposal of palm oil industrial waste has led to serious environmental pollution. In this study, we isolated Paenibacillus macerans strain I6, which can degrade oil palm empty fruit bunches generated by the palm oil industry in nutrient-free water, from bovine manure biocompost and sequenced its genome on PacBio RSII and Illumina NovaSeq 6000 platforms. We obtained 7.11 Mbp of genomic sequences with 52.9% GC content from strain I6. Strain I6 was phylogenetically closely related to P. macerans strains DSM24746 and DSM24 and was positioned close to the head of the branch containing strains I6, DSM24746, and DSM24 in the phylogenetic tree. We used the RAST (rapid annotation using subsystem technology) server to annotate the strain I6 genome and discovered genes related to biological saccharification; 496 genes were related to carbohydrate metabolism and 306 genes were related to amino acids and derivatives. Among them were carbohydrate-active enzymes (CAZymes), including 212 glycoside hydrolases. Up to 23.6% of the oil palm empty fruit bunches was degraded by strain I6 under anaerobic and nutrient-free conditions. Evaluation of the enzymatic activity of extracellular fractions of strain I6 showed that amylase and xylanase activity was highest when xylan was the carbon source. The high enzyme activity and the diversity in the associated genes may contribute to the efficient degradation of oil palm empty fruit bunches by strain I6. Our results indicate the potential utility of P. macerans strain I6 for lignocellulosic biomass degradation.
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Actin cytoskeletal inhibitor 19,20-epoxycytochalasin Q sensitizes yeast cells lacking ERG6 through actin-targeting and secondarily through disruption of lipid homeostasis
(2021-12-01)
Watchaputi, Kwanrutai
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Somboon, Pichayada
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Phromma-in, Nipatthra
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Ratanakhanokchai, Khanok
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Soontorngun, Nitnipa
Repetitive uses of antifungals result in a worldwide crisis of drug resistance; therefore, natural fungicides with minimal side-effects are currently sought after. This study aimed to investigate antifungal property of 19, 20-epoxycytochalasin Q (ECQ), derived from medicinal mushroom Xylaria sp. BCC 1067 of tropical forests. In a model yeast Saccharomyces cerevisiae, ECQ is more toxic in the erg6∆ strain, which has previously been shown to allow higher uptake of many hydrophilic toxins. We selected one pathway to study the effects of ECQ at very high levels on transcription: the ergosterol biosynthesis pathway, which is unlikely to be the primary target of ECQ. Ergosterol serves many functions that cholesterol does in human cells. ECQ’s transcriptional effects were correlated with altered sterol and triacylglycerol levels. In the ECQ-treated Δerg6 strain, which presumably takes up far more ECQ than the wild-type strain, there was cell rupture. Increased actin aggregation and lipid droplets assembly were also found in the erg6∆ mutant. Thereby, ECQ is suggested to sensitize yeast cells lacking ERG6 through actin-targeting and consequently but not primarily led to disruption of lipid homeostasis. Investigation of cytochalasins may provide valuable insight with potential biopharmaceutical applications in treatments of fungal infection, cancer or metabolic disorder.
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Chemical pretreatment-independent saccharifications of xylan and cellulose of rice straw by bacterial weak lignin-binding xylanolytic and cellulolytic enzymes
(2017-11-01)
Teeravivattanakit, Thitiporn
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Baramee, Sirilak
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Phitsuwan, Paripok
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Sornyotha, Somphit
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Waeonukul, Rattiya
Complete utilization of carbohydrate fractions is one of the prerequisites for obtaining economically favorable lignocellulosic biomass conversion. This study shows that xylan in untreated rice straw was saccharified to xylose in one step without chemical pretreatment, yielding 58.2% of the theoretically maximum value by Paenibacillus curdlanolyticus B-6 PcAxy43A, a weak lignin-binding trifunctional xylanolytic enzyme, endoxylanase/β-xylosidase/arabinoxylan arabinofuranohydrolase. Moreover, xylose yield from untreated rice straw was enhanced to 78.9% by adding endoxylanases PcXyn10C and PcXyn11A from the same bacterium, resulting in improvement of cellulose accessibility to cellulolytic enzyme. After autoclaving the xylanolytic enzyme-treated rice straw, it was subjected to subsequent saccharification by a combination of the Clostridium thermocellum endoglucanase CtCel9R and Thermoanaerobacter brockii β-glucosidase TbCglT, yielding 88.5% of the maximum glucose yield, which was higher than the glucose yield obtained from ammoniatreated rice straw saccharification (59.6%). Moreover, this work presents a new environment-friendly xylanolytic enzyme pretreatment for beneficial hydrolysis of xylan in various agricultural residues, such as rice straw and corn hull. It not only could improve cellulose saccharification but also produced xylose, leading to an improvement of the overall fermentable sugar yields without chemical pretreatment.
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Multifunctional properties of glycoside hydrolase family 43 from Paenibacillus curdlanolyticus strain B-6 including exo-β-xylosidase, endo-xylanase, and α-L-arabinofuranosidase activities
(2015-01-01)
Wongratpanya, Kanok
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Imjongjairak, Siriluck
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Waeonukul, Rattiya
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Sornyotha, Somphit
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Phitsuwan, Paripok
The glycoside hydrolase family 43 from Paenibacillus curdlanolyticus strain B-6 (GH43B6) exhibited multifunctional properties, including exo-β-xylosidase, endo-xylanase, and α-L-arabinofuranosidase enzymatic activities. GH43B6 released xylose as a hydrolysis product from the successive reduction of xylooligosaccharides as a result of exo-β-xylosidase activity. Moreover, GH43B6 also predominantly released xylose from low-substituted xylan derived from birchwood. However, when the highly substituted rye flour arabinoxylan was used as a substrate, exo-β-xylosidase activity changed to endo-xylanase activity, indicating that the enzymatic property of GH43B6 is influenced by the substituted side groups of xylan. For α-L-arabinofuranosidase, arabinose was released from short-chain substrates including p-nitrophenyl-α-L-arabinofuranoside and α-L-Araf-(1→2)-[α-L-Araf-(1→3)]-β-D-Xylp. This study reports the novel trifunctional properties of GH43B6 containing exo- and endo-activity together with xylanolytic debranching enzymatic activity, which increases its potential for application in lignocellulose-based biorefineries.
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Symbiotic Behavior during Co-culturing of Clostridium thermocellum NKP-2 and Thermoanaerobacterium thermosaccharolyticum NOI-1 on Corn Hull
(2014-05-01)
Chimtong, Suphavadee
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Tachaapaikoon, Chakrit
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Sornyotha, Somphit
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Pason, Patthra
;
Waeonukul, Rattiya
The symbiosis of co-culturing between Clostridium thermocellum NKP-2 and Thermoanaerobacterium thermosaccharolyticum NOI-1 is described. An efficient biomass-degrading enriched culture was isolated from soil that contained two different bacterial strains showing homology to C. thermocellum and T. thermosaccharolyticum. The enzymatic system produced from the isolated strains when cultivated individually on corn hulls demonstrated different cellulolytic and xylanolytic enzyme activities. Strain NKP-2 produced cellulose- and xylan-main chain cleaving enzymes such as carboxymethylcellulase (CMCase), avicelase, and xylanase as major enzymes, whereas strain NOI-1 produced primarily short- and side-chain cleaving enzymes such as cellobiohydrolase, β-glucosidase, β-xylosidase, acetyl esterase, and especially α-L-arabinofuranosidase. Enhancement of corn hull utilization, cell growth, and fermentation products (ethanol, butanol, acetic acid, butyric acid, H2, and CO2) was greatly increased during co-culturing compared with individual cultivation of both strains. The symbiotic behavior between both strains was one of mutualism, in which the synergistic degradation of corn hulls by co-action of cellulolytic and xylanolytic enzymes promoted hydrolysis of biomass for growth and fermented products.

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