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Biochemistry Dec 2023A crucial prerequisite for industrial applications of enzymes is the maintenance of specific activity across wide thermal ranges. β-Glucosidase (EC 3.2.1.21) is an...
A crucial prerequisite for industrial applications of enzymes is the maintenance of specific activity across wide thermal ranges. β-Glucosidase (EC 3.2.1.21) is an essential enzyme for converting cellulose in biomass to glucose. While the reaction mechanisms of β-glucosidases from various thermal ranges (hyperthermophilic, thermophilic, and mesophilic) are similar, the factors underlying their thermal sensitivity remain obscure. The work presented here aims to unravel the molecular mechanisms underlying the thermal sensitivity of the enzymatic activity of the β-glucosidase BglB from the bacterium . Experiments reveal a maximum enzymatic activity at 315 K, with a marked decrease in the activity below and above this temperature. Employing simulations, we identified the crucial role of the active site tunnel residues in the thermal sensitivity. Specific tunnel residues were identified via energetic decomposition and protein-substrate hydrogen bond analyses. The experimentally observed trends in specific activity with temperature coincide with variations in overall binding free energy changes, showcasing a predominantly electrostatic effect that is consistent with enhanced catalytic pocket-substrate hydrogen bonding (HB) at . The entropic advantage owing to the HB substate reorganization was found to facilitate better substrate binding at 315 K. This study elicits molecular-level insights into the associative mechanisms between thermally enabled fluctuations and enzymatic activity. Crucial differences emerge between molecular mechanisms involving the actual substrate (cellobiose) and a commonly employed chemical analogue. We posit that leveraging the role of fluctuations may reveal unexpected insights into enzyme behavior and offer novel paradigms for enzyme engineering.
Topics: beta-Glucosidase; Cellulose; Catalytic Domain; Temperature; Glucose; Substrate Specificity
PubMed: 37997958
DOI: 10.1021/acs.biochem.3c00387 -
Bioresource Technology Feb 2024Recent decarbonization efforts have led to interests in producing more bio-based chemicals. One attractive compound produced biochemically is the platform chemical known...
Recent decarbonization efforts have led to interests in producing more bio-based chemicals. One attractive compound produced biochemically is the platform chemical known as 2,3-butanediol (2,3-BDO). In this work a mild alkaline pretreatment using sodium carbonate was performed on corn stover (CS) and switchgrass (SG) to generate hydrolysates for fermentation with the 2,3-BDO producer bacteria strain Paenibacillius polymyxa. Enzymatic hydrolysis performed on the pretreated CS and SG produced theoretical sugar yields of 80 % and 95 % for glucose and xylose, respectively. Fermentations with P. polymxya conducted in anaerobic bottles produced 2,3-BDO reaching concentrations ranging from 14 to 18 g/L with negligible conversion into acetoin. Bioreactor fermentations using the hydrolysate media generated up to 43 g/L and 34 g/L of 2,3-BDO from pretreated CS and SG, respectively, within 24 h of fermentation. However, 2,3-BDO product output was reduced by 40-50 % over the remainder of the fermentation due to conversion into acetoin caused by glucose depletion.
Topics: Fermentation; Paenibacillus polymyxa; Acetoin; Butylene Glycols; Glucose
PubMed: 37993069
DOI: 10.1016/j.biortech.2023.130053 -
Plants (Basel, Switzerland) Oct 2023Clubroot is one of the most serious soil-borne diseases on crucifer crops worldwide. Seed treatment with biocontrol agents is an effective and eco-friendly way to...
Clubroot is one of the most serious soil-borne diseases on crucifer crops worldwide. Seed treatment with biocontrol agents is an effective and eco-friendly way to control clubroot disease. However, there is a big challenge to inoculating the seed with bacterial cells through seed pelleting due to the harsh environment on the seed surface or in the rhizosphere. In this study, a method for microbial seed pelleting was developed to protect pak choi seedlings against clubroot disease. Typically, a biocontrol bacterium, ZF129, was encapsulated by the spray-drying method with gum arabic as wall material, and then pak choi seeds were pelleted with the microencapsulated ZF129 (ZF129m). The morphology, storage stability, and release behavior of ZF129 microcapsules were evaluated. Compared with the naked ZF129 cells, encapsulated ZF129 cells showed higher viability during ambient storage on pak choi seeds. Moreover, ZF129m-pelleted seeds showed higher control efficacy (71.23%) against clubroot disease than that of nonencapsulated ZF129-pelleted seeds (61.64%) in pak choi. Seed pelleting with microencapsulated biocontrol ZF129 proved to be an effective and eco-friendly strategy for the control of clubroot disease in pak choi.
PubMed: 37960058
DOI: 10.3390/plants12213702 -
Bioresource Technology Jan 20242,3-Butanediol is an essential renewable fuel. The synthesis of 2,3-butanediol using Paenibacillus polymyxa has attracted increasing attention. In this study, the...
2,3-Butanediol is an essential renewable fuel. The synthesis of 2,3-butanediol using Paenibacillus polymyxa has attracted increasing attention. In this study, the glucose-derived 2,3-butanediol pathway and its related genes were identified in P. polymyxa using combined transcriptome and metabolome analyses. The functions of two distinct genes ldh1 and ldh3 encoding lactate dehydrogenase, the gene bdh encoding butanediol dehydrogenase, and the spore-forming genes spo0A and spoIIE were studied and directly knocked out or overexpressed in the genome sequence to improve the production of 2,3-butanediol. A raw hydrolysate of poplar wood containing 27 g/L glucose and 15 g/L xylose was used to produce 2,3-butanediol with a maximum yield of 0.465 g/g and 93 % of the maximum theoretical value, and the total production of 2,3-butanediol and ethanol reached 21.7 g/L. This study provides a new scheme for engineered P. polymyxa to produce renewable fuels using raw poplar wood hydrolysates.
Topics: Paenibacillus polymyxa; Fermentation; Metabolic Engineering; Butylene Glycols; Glucose; Paenibacillus
PubMed: 37956945
DOI: 10.1016/j.biortech.2023.130002 -
Letters in Applied Microbiology Nov 2023Paenibacillus polymyxa is an important biocontrol bacterium. The combination of propidium monoazide (PMA) and quantitative polymerase chain reactionq (qPCR) has proven...
Paenibacillus polymyxa is an important biocontrol bacterium. The combination of propidium monoazide (PMA) and quantitative polymerase chain reactionq (qPCR) has proven effective in quantifying live bacteria from various microorganisms. The objective was to create a PMA-qPCR assay to precisely and consistently measure the number of living bacteria of biocontrol P. polymyxa. The primers were designed for the spo0A gene of P. polymyxa HY96-2. The optimal conditions for treating the target strain with PMA were a PMA concentration of 15 μg/mL, an incubation time of 5 min, and an exposure time of 10 min. The PMA-qPCR method had a limit of quantification (LOQ) of 1.0 × 103 CFU/mL for measuring the amount of viable P. polymyxa bacteria. The PMA-qPCR method is more sensitive than the qPCR method in detecting viable bacteria in the mixtures of viable and dead bacteria. The accuracy and reproducibility of quantifying viable P. polymyxa bacteria using the PMA-qPCR method were higher compared to the plate count method.
Topics: Paenibacillus polymyxa; Reproducibility of Results; Biological Assay; Bacteria
PubMed: 37952090
DOI: 10.1093/lambio/ovad127 -
Pest Management Science Mar 2024Root knot nematodes cause great damage to crops worldwide. Due to the negative effects of the application of fumigant and old chemical nematicides, biological...
BACKGROUND
Root knot nematodes cause great damage to crops worldwide. Due to the negative effects of the application of fumigant and old chemical nematicides, biological nematicides have drawn increasing attention in recent years. Here we tested the fumigant activity of the volatile organic compounds (VOCs) blends emitted from Paenibacillus polymyxa and pure commercial VOCs against M. incognita.
RESULTS
In this study, we investigated whether P. polymyxa strain J2-4 could produce VOCs that exhibit nematicidal activity. In vitro assays indicated that J2-4 VOCs were highly toxic to second stage juveniles (J2s) and could inhibit egg hatching. Three-layered pot experiments showed that the number of nematodes that penetrating in cucumber roots was reduced by 69.27% after the application of J2-4 VOCs under greenhouse conditions. We identified 14 volatiles using solid-phase micro-extraction gas chromatography-mass spectrometry. The efficacy of six commercially available VOCs, namely 2-isobutyl-3-methylpyrazine, 2,4-dimethoxybenzaldoxime, 2-dodecanone, 2-tridecanol, 2-tridecanone, and 2-tetradecanol, against M. incognita were examined. Except for 2,4-dimethoxybenzaldoxime, the remaining five VOCs showed strong direct-contact nematicidal activity against J2s of M. incognita, and only 2-isobutyl-3-methylpyrazine showed strong fumigant activity against J2s of M. incognita. In pot experiments, 2-isobutyl-3-methylpyrazine and 2-dodecanone reduced the number of root galls by about 70%, and 2-tridecanone reduced the number of root galls and egg masses by about 63% compared with controls.
CONCLUSION
Paenibacillus polymyxa strain J2-4 exhibited high fumigant activity against M. incognita. Our results provide evidence for the use of J2-4 and its VOCs as biocontrol agents in the management of root-knot nematodes. © 2023 Society of Chemical Industry.
Topics: Animals; Tylenchoidea; Volatile Organic Compounds; Paenibacillus polymyxa; Solanum lycopersicum; Antinematodal Agents; Pesticides; Ketones
PubMed: 37899496
DOI: 10.1002/ps.7859 -
Poultry Science Dec 2023Nanomedicine is a critical therapeutic approach for treating most poultry illnesses, particularly parasitic infections. Coccidiosis is a severe protozoan infection...
Supplementing broiler diets with bacterial selenium nanoparticles enhancing performance, carcass traits, blood indices, antioxidant status, and caecal microbiota of Eimeria tenella-infected broiler chickens.
Nanomedicine is a critical therapeutic approach for treating most poultry illnesses, particularly parasitic infections. Coccidiosis is a severe protozoan infection affecting poultry; the emergence of drug-resistant Eimeria strains demands the development of new, safe therapies. Consequently, the objective of this work was to investigate the efficacy of the biosynthesized selenium nanoparticles (SeNPs) by Paenibacillus polymyxa (P. polymyxa) against Eimeria tenella (E. tenella) experimental infection in broiler chickens. The prepared SeNPs absorbed the UV at 270 nm were spherical with a size of 26 nm, and had a surface negative charge of -25 mV. One hundred and fifty, 1-day-old male broiler chicks were randomly allocated into 5 groups (30 birds/group with triplicates each) as follows: T1: negative control (noninfected and nontreated with SeNPs); T2: delivered SeNPs (500 µg/kg diet) for 35 successive days, T3: E. tenella-infected (positive control birds), T4: E. tenella-infected and treated with SeNPs (500 µg/kg diet) and T5: E. tenella-infected chicks and treated with anticoccidial agent (sulfadimidine, 16% solution 8 mL/L of drinking water) for 5 successive days. At 14 d of age, each bird in infected groups was orally treated with 3 × 10 sporulated oocyst of E. tenella. SeNPs considerably decreased the number of oocysts in broiler feces compared to positive control and anticoccidial drug, followed by a substantial reduction of parasite phase count in the cecum (15, 10, and 8 for meronts, gamonts, and developing oocysts) when compared with positive control birds. The Eimeria experimental infection lowered the activity of antioxidant enzymes, superoxide dismutase (SOD), glutathione peroxidase (GPx), and reduced glutathione (GSH) while increasing the stress parameters nitric oxide (NO) and malonaldehyde (MDA). Moreover, the production of proinflammatory (TNF-α and IL-6) and apoptotic genes (BcL2 and Cas-3) were significantly elevated. Administrating SeNPs to chicks significantly decreased oxidative stress, inflammation, and apoptotic markers in the cecum tissue. Therefore, growth performance, carcass weights, antioxidant enzymes, and blood properties of infected chicks were enhanced. The findings compared the protecting role of Se-nanoparticles against cecum damages in E. tenella-infected broilers.
Topics: Animals; Male; Eimeria tenella; Chickens; Antioxidants; Selenium; Coccidiosis; Diet; Eimeria; Cecum; Poultry Diseases; Oocysts
PubMed: 37866222
DOI: 10.1016/j.psj.2023.103111 -
Plant Science : An International... Dec 2023Drought has become the most important limiting factor to crop productions. Research thus far has been devoted to identifying drought-responsive genes (DRGs) via breeding...
Drought has become the most important limiting factor to crop productions. Research thus far has been devoted to identifying drought-responsive genes (DRGs) via breeding and engineering approaches. Still, these efforts have not resulted in a solution to combat drought's effects because the ectopic expression of most DRGs causes adverse effects that reduce plant growth and yields. Lately, we discovered that two DRGs, Response to Desiccation (RD)29A and RD29B, induced by Paenibacillus polymyxa CR1, a plant growth-promoting rhizobacterium capable of priming drought tolerance and concurrently stimulating plant growth, play pivotal roles in defense responses against drought. In this study, we employ the ChlP and qRT-PCR analyses and further clarify that P. polymyxa CR1 reformats the chromatin/transcriptional memory of RD29s, positioned as upstream controllers that fine-tune the temporal dynamic of stress-regulating transcription factors (TFs) in elaborating induced systemic drought tolerance without growth penalties. Two genes coordinate the upregulation of NAC TFs, while feedback inhibiting CBF TFs, which regulate downstream DRG expressions. This supports that RD29s are unique, feasible transgene candidates for improving plants' survival capacity in both optimal and drought conditions. However, the mode of action of RD29A and RD29B are partly independent, exerting distinct roles in disparate ecological states. When subjected to increasing NaCl concentrations, the KO mutant of RD29A (rd29a) displayed enhanced tolerance compared to WT and rd29b plants, proposing that RD29B, but not RD29A, a key player in conferring WT-like tolerance to salinity stress; further studies will be needed to optimize/maximize their applications in engineering for-profit drought and/or broad-spectrum stress tolerant crops.
Topics: Droughts; Arabidopsis Proteins; Arabidopsis; Gene Expression Regulation, Plant; Salinity; Paenibacillus; Epigenesis, Genetic; Transcription Factors; Plants, Genetically Modified; Stress, Physiological; Genetic Markers
PubMed: 37838156
DOI: 10.1016/j.plantsci.2023.111895 -
Frontiers in Microbiology 2023Fusaricidin, a lipopeptide antibiotic, is specifically produced by strains, which could strongly inhibit fungi. Fusaricidin bio-synthetase A (FusA) is composed of six...
Fusaricidin, a lipopeptide antibiotic, is specifically produced by strains, which could strongly inhibit fungi. Fusaricidin bio-synthetase A (FusA) is composed of six modules and is essential for synthesizing the peptide moiety of fusaricidin. In this study, we confirmed the FusA of strain WLY78 involved in producing Fusaricidin LI-F07a. We constructed six engineered strains by deletion of each module within FusA from the genome of strain WLY78. One of the engineered strains is able to produce a novel compound that exhibits better antifungal activity than that of fusaricidin LI-F07a. This new compound, known as fusaricidin [ΔAla] LI-F07a, has a molecular weight of 858. Our findings reveal that it exhibits a remarkable 1-fold increase in antifungal activity compared to previous fusaricidin, and the fermentation yield reaches ~55 mg/L. This research holds promising implications for plant protection against infections caused by and pathogen infection.
PubMed: 37822742
DOI: 10.3389/fmicb.2023.1239958 -
Microbiology Resource Announcements Nov 2023Here, we report 10 distinct bacterial genomes from Amazonian dark earths, including six identified as , while the remaining four were unique representatives of , , , and...
Here, we report 10 distinct bacterial genomes from Amazonian dark earths, including six identified as , while the remaining four were unique representatives of , , , and sp., respectively. Each strain exhibited antagonistic activity against , underscoring their potential as sustainable agriculture resources.
PubMed: 37811974
DOI: 10.1128/MRA.00574-23