Biomolecules
·
2025
·Vol. 15
·期 12
·1694
·
IF 4.8
Siyu Huang,Xiaorui Li,Xin Lu,Biao Kan
Polymyxins, including polymyxin B (PMB), are last-resort antibiotics against multidrug-resistant Gram-negative infections in humans and livestock. Residual polymyxins from wastewater and manure can accumulate in soil, facilitating the emergence and spread of polymyxin resistance.Paenibacillus polymyxa, a natural polymyxin producer used in crop cultivation, may increase soil polymyxin burden. Since PMB strongly adsorbs to soil, its reliable quantification has been challenging. To address this, the extraction solvent and solid-phase extraction procedure were optimized to improve recovery and reduce matrix effects. We developed and validated a UPLC-MS/MS method to quantify PMB in soil. The method showed linearity (10–1000 ng/g), with a limit of detection of 0.86 ng/g and a limit of quantification of 2.12 ng/g. Method validation confirmed acceptable analytical performance. A 28-day monitoring of PMB in soil inoculated with varyingP. polymyxadoses revealed a dose-dependent increase over the first 14 days, followed by a decline; PMB remained detectable on day 28. Ecological risk assessment using the risk quotient (RQ) indicated that PMB levels in the high-dose group (2 × 108CFU/100 g) approached the high-risk threshold (RQ ≥ 1) on day 14, while lower doses posed low to medium risk. This work provides a soil PMB quantification method and insight into the ecological risk ofP. polymyxaapplication.
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JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
·
2026
·
IF 6.7
Binhao Wang,Zhaoyue Fan,Jie Zhang,Ulrich Schwaneberg,Ye Ni,Ruizhi Han
Cyclodextrin glycosyltransferase (CGTase) is widely used in stevioside glycosylation, yet achieving precise regioselectivity remains a persistent challenge. Here, 200 ns molecular dynamics (MD) simulations identified residue Y260 in Paenibacillus macerans CGTase as a conformation-sensitive determinant for rebaudioside A (RebA) glycosylation. The Y260N variant achieved exclusive regioselectivity, producing only the C13-glycosylated products of RebA, although with a ∼30% reduction in conversion compared with wild-type. This high regioselectivity extended to other steviol glycosides─Reb C, D, and M─each yielding a single regioisomer. Further MD simulations indicated that conformational reorganization restricts access to O21 and stabilizes Glu258 toward O14, thereby enforcing C13-specific glycosylation. This work elucidates a mechanism for regioselective regulation in CGTase and provides a strategy for engineering other glycosylation enzymes.
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Microbial Cell Factories
·
2026
·Vol. 25
·期 1
·117
·
IF 5.8
Deng Yun,Niu Yuqing,Xu Qing,Xie DongRong,Su Yan,Liu DuanHua,Chen Yong-He,Han YongHe,Tian Dagang
Background The widespread use and environmental persistence of the herbicide glyphosate raise significant concerns for human and ecological health. Developing efficient and sustainable remediation strategies is therefore crucial. Microbial degradation and biocontrol are two promising approaches. This study aimed to isolate and characterize a bacterial strain capable of both degrading glyphosate and antagonizing soil-borne fungal pathogens, and to evaluate its impact on soil microbial communities. Results This study isolated and characterized a novel bacterial strain, NPDY10, identified as Paenibacillus ottowii , which exhibits dual beneficial functions: efficient glyphosate degradation and broad-spectrum antagonism against soil-borne fungal pathogens. Under optimal conditions (pH 7–7.5, 30–35 °C), strain NPDY10 completely degraded 400 mg L⁻¹ of glyphosate within four days, utilizing the herbicide as a carbon source. Metabolic profiling via UPLC-MS/MS confirmed glyphosate degradation via the aminomethylphosphonic acid (AMPA) pathway In a rice paddy field trial, the application of NPDY10 reduced glyphosate levels in paddy water, and a visible foam layer formed, serving as a visual indicator of active metabolism. Furthermore, strain NPDY10 demonstrated broad-spectrum antifungal activity in vitro, inhibiting 17 plant-pathogenic fungi with inhibition rates ranging from 60.00% to 92.00%. Analysis of soil microbial communities in a subsequent maize cultivation season revealed that NPDY10 treatment increased bacterial diversity and suppressed the relative abundance of pathogenic fungal genera such as Fusarium and Gibberella . Conclusion Paenibacillus ottowii NPDY10 represents a promising multi-functional agent for sustainable agriculture, potentially combining glyphosate bioremediation with direct and indirect biocontrol effects through modulation of soil microbial communities, thereby contributing to improved soil health.
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APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
·
2024
·Vol. 108
·期 1
·1-13
·
IF 3.9
Wu Zongzhan,Dou Wenyu,Yang Xiaolin,Niu Tengfei,Han Zhuzhen,Yang Li,Wang Rufeng,Wang Zhengtao
Abstract Oleanane-type ginsenosides are a class of compounds with remarkable pharmacological activities. However, the lack of effective preparation methods for specific rare ginsenosides has hindered the exploration of their pharmacological properties. In this study, a novel glycoside hydrolase Pl GH3 was cloned from Paenibacillus lactis 154 and heterologous expressed in Escherichia coli . Sequence analysis revealed that Pl GH3 consists of 749 amino acids with a molecular weight of 89.5 kDa, exhibiting the characteristic features of the glycoside hydrolase 3 family. The enzymatic characterization results of Pl GH3 showed that the optimal reaction pH and temperature was 8 and 50 °C by using p -nitrophenyl- β - d -glucopyranoside as a substrate, respectively. The K m and k cat values towards ginsenoside Ro were 79.59 ± 3.42 µM and 18.52 s −1 , respectively. Pl GH3 exhibits a highly specific activity on hydrolyzing the 28- O - β - d -glucopyranosyl ester bond of oleanane-type saponins. The mechanism of hydrolysis specificity was then presumably elucidated through molecular docking. Eventually, four kinds of rare oleanane-type ginsenosides (calenduloside E, pseudoginsenoside RP1, zingibroside R1, and tarasaponin VI) were successfully prepared by biotransforming total saponins extracted from Panax japonicus . This study contributes to understanding the mechanism of enzymatic hydrolysis of the GH3 family and provides a practical route for the preparation of rare oleanane-type ginsenosides through biotransformation. Key points • The glucose at C-28 in oleanane-type saponins can be directionally hydrolyzed. • Mechanisms to interpret PlGH3 substrate specificity by molecular docking. • Case of preparation of low-sugar alternative saponins by directed hydrolysis.
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INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
·
2024
·
IF 7.7
Huajun Kang,Tengfei Fan,Zihan Lin,Yanxia Shi,Xuewen Xie,Lei Li,Sheng Xiang,Xiaowei Yuan,Xingsheng Li,Baoju Li,Ali Chai
Clubroot, caused by the obligate parasite Plasmodiophora brassicae , is one of the most important diseases of brassicas. The antagonistic bacterium Paenibacillus polymyxa ZF129 can suppress clubroot while its effectiveness is often unstable. To control clubroot more effectively, the macrobeads for controlled release of ZF129 were prepared using microencapsulation technology. Macrobeads with various ratios of chitosan (2 % w/w): carrageenan (0.3 % w/v) were prepared by an ionotropic gelation method and the bacteria ZF129 was loaded into macrobeads. The 1:1 chitosan: carrageenan showed the maximum swelling ratio (634 %), and the maximum survival rate (61.52 ± 1.12 %) after freeze-drying. Fourier transform infrared revealed the electrostatic interactions between chitosan and carrageenan. The macrobeads can efficiently release ZF129 strains into phosphate buffer solution and reach equilibrium in 48 h. The maximum number of bacteria cells to be released in the soil was observed after 25–30 days. The control efficacy of ZF129 macrobeads (chitosan: carrageenan, 1:1) and ZF129 culture against clubroot disease was 76.33 ± 3.65 % and 59.76 ± 4.43 % in greenhouse experiments, respectively and the control efficacy was calculated as 60.74 ± 5.00 % for ZF129 macrobeads and 40.94 ± 4.05 % for ZF129 culture under field experiments, respectively. The ZF129 macrobeads had significant growth-promoting effects on pak choi and Chinese cabbage. The encapsulation method described in this study is a prudent approach toward efficient biopesticides utilization with reduced environmental implications.
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JOURNAL OF MOLECULAR LIQUIDS
·
2024
·
IF 5.3
Fanjin Meng,Xin Ju,Yuyang Zhou,Lishi Yan,Zhi Chen,Yuqiu Wu,Liangzhi Li
The two major impediments to biomass resourcing are the catalytic efficiency of enzymes and the effectiveness of biomass pretreatment. In this study, six genes encoding β-Glucosidases (BGLs) derived from Paenibacillus sp. LLZ1 were cloned and expressed. The activity of BGL-F, which had the highest enzyme activity, was 24.1 U/mg, which was 39.8–83.7% higher than that of the other BGLs. Molecular docking and surface charge analyses showed that the binding energy of BGL-F to cellobiose and its electronegative ligand-binding pocket were greater than those of other BGLs. On the other hand, by calculating and comparing the Kamlet–Taft (KT) values of deep eutectic solvent (DES) composed of different hydrogen bond donors (HBD) and hydrogen bond acceptors (HDA), it was found that DES composed of betaine and glycerol had the highest α value of 0.97, meaning that it could provide the highest hydrogen bonding capacity, and thus it had the best pretreatment effect on biomass. Analysis by circular dichroism (CD) spectroscopy revealed a decrease in α-helix and an increase in β-strand in the secondary structure of the DES-treated BGL-F, implying an increase in enzyme activity and stability. This result was also confirmed experimentally by the fact that the K m and V max of the enzyme in the DES system increased by 13.2% and 57.9%, respectively, and the inactivation rate (k d ) decreased by 21.4%. The results of this study showed that DES consisting of glycerol-betaine achieved a better balance between the promotion of enzyme activity and biomass pretreatment.
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Synthetic and Systems Biotechnology
·
2024
·
IF 4.4
Hui-Zhong Sun,Si-Yu Wei,Qiu-Man Xu,Wei Shang,Qing Li,Jing-Sheng Cheng,Ying-Jin Yuan
Polymyxin B, produced by Paenibacillus polymyxa, is used as the last line of defense clinically. In this study, exogenous mixture of precursor amino acids increased the level and proportion of polymyxin B1 in the total of polymyxin B analogs of P. polymyxa CJX518-AC (PPAC) from 0.15 g/L and 61.8 % to 0.33 g/L and 79.9 %, respectively. The co-culture of strain PPAC and recombinant Corynebacterium glutamicum -leu01, which produces high levels of threonine, leucine, and isoleucine, increased polymyxin B1 production to 0.64 g/L. When strains PPAC and C. glu -leu01 simultaneously inoculated into an optimized medium with 20 g/L peptone, polymyxin B1 production was increased to 0.97 g/L. Furthermore, the polymyxin B1 production in the co-culture of strains PPAC and C. glu -leu01 increased to 2.21 g/L after optimized inoculation ratios and fermentation medium with 60 g/L peptone. This study provides a new strategy to improve polymyxin B1 production.
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Biology-Basel
·
2025
·Vol. 14
·期 4
·375
·
IF 3.5
Jiayi Ma,Jialin Liu,Yanxia Shi,Xuewen Xie,Ali Chai,Sheng Xiang,Xianhua Sun,Lei Li,Baoju Li,Tengfei Fan
In this study, a Paenibacillus polymyxa ZF129 microcapsule suspension (CS-ZF129) was prepared. P. polymyxa ZF129 was microencapsulated by gum arabic via the spray-drying method. Coating seeds with the CS-ZF129 not only increased the control efficacy against cucumber root rot to 46.30 ± 0.02%, but also promoted the growth of the cucumber roots and other aspects, effectively improving the colonization ability of polymyxa ZF129 in the cucumber root system, which was analyzed to clarify the biological control mechanism of the cucumber Fusarium root rot disease through the enzyme activity. This study provides an efficient means based on seed coating for the biological control of cucumber Fusarium root rot. Fusarium root rot, a destructive soil-borne fungal disease, necessitates eco-friendly biocontrol strategies. This study developed a microbial seed-coating approach using the antagonistic strain Paenibacillus polymyxa ZF129, formulated into a microencapsulated powder (10 8 CFU/g) and a suspension (CS-ZF129). CS-ZF129 application enhanced cucumber resistance, achieving 46.30 ± 0.02% disease suppression while promoting root growth. The maximum increase in the fresh weight of the root in the promotion of rectangular growth was 47.16%. The colonization dynamics of ZF129 in the rhizosphere were systematically tracked, revealing its antagonistic correlation with Fusarium proliferation. An enzymatic activity analysis further uncovered the underlying regulatory mechanisms, demonstrating induced defense responses through pathogenesis-related protein activation. These findings highlight ZF129’s dual functionality as a biocontrol agent and a plant growth promoter, offering a sustainable strategy against soil-borne pathogens.
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BMC MICROBIOLOGY
·
2026
·
IF 5.4
Shi Le-Nan,Han Yang-gang,Liang Hai,Li Tiejun,Shi Hui,Jin Lei
Background The rapid expansion of the aquaculture industry has intensified the discharge of nitrogen-rich wastewater, posing significant ecological risks. Biological treatment with HN-AD bacteria is sustainable, but most conventional strains lack long-term environmental resilience. The key bottleneck is identifying novel, robustly adaptable strains, especially spore-forming Gram-positive bacteria. Moreover, the non-canonical metabolic mechanisms that distinguish such strains remain largely unexplored. This study isolated a novel HN-AD strain, Paenibacillus glycanilyticus DQ-1, from aquaculture sludge and investigated its nitrogen removal performance and genomic metabolic pathways. Methods Strain DQ-1 was isolated and identified through 16 S rRNA gene sequencing and morphological analysis. Its nitrogen removal efficiency was evaluated under aerobic conditions with different nitrogen sources, including ammonium nitrogen (NH₄ + -N), nitrate nitrogen (NO₃ − -N), total inorganic nitrogen (TIN) and hydroxylamine nitrogen (NH 2 OH-N). Whole-genome sequencing was conducted using the PacBio Sequel II platform to identify functional genes and reconstruct the nitrogen metabolic pathways. Results Strain DQ-1 achieved 93.26% NH₄⁺-N and 100% NO₃⁻-N removal within 36 h, with 95.92% TIN removal. Genomic analysis revealed a complete assimilatory nitrate reduction pathway ( nasAB and nirBD ). Notably, while the canonical hydroxylamine oxidoreductase gene ( hao ) is absent, the strain showed 74.67% NH 2 OH-N removal and harbors a putative ammonia monooxygenase gene ( amo ). These results suggest that DQ-1 employs a novel non-canonical pathway, distinct from known HN-AD models, for efficient nitrogen transformation. Conclusions P. glycanilyticus DQ-1 differs from typical HN-AD bacteria in its spore-forming ability and a novel hao -independent pathway. This study provides the first comprehensive genomic insight into the nitrogen removal capacity of P. glycanilyticus , expanding the microbial resource pool for sustainable environmental remediation.
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PLANT PATHOLOGY
·
2015
·Vol. 64
·期 5
·1041-1052
·
IF 2.121
W. Raza,J. Yuan,Y. C. Wu,F. U. Rajer,Q. Huang,S. Qirong
The aim of the present study was to investigate the effects of the phytotoxin fusaric acid (FA) on the biocontrol traits of two biocontrol strains Paenibacillus polymyxa WR-2 and SQR-21. The results showed that the growth of both WR-2 and SQR-21 decreased with increasing FA concentration, and at 70 and 80 μ g mL −1 FA, respectively, the strains were unable to grow. The biocontrol traits of both strains were negatively affected by FA concentration higher than 2·5 μ g mL −1 . However, at 2·5 μ g mL −1 FA, biofilm formation and root colonization were not affected and there was even a positive effect on the production of spores and hydrolytic enzymes (protease and β -l,3-glucanase). The production of fusaricidin-type antifungal compounds was increased with an increase in FA concentration up to 50 and 60 μ g mL −1 for WR-2 and SQR-21, respectively. The production of antifungal volatile organic compounds by WR-2 and SQR-21 was increased only at 2·5 μ g mL −1 FA. The effect of FA on the overall metabolic activity of WR-2 and SQR-21 was also determined. This study will help to understand the response of P. polymyxa strains to FA and will help to improve their biocontrol efficiency.
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APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
·
2019
·Vol. 190
·期 3
·826-838
·
IF 2.14
Liu Hang,Zhou Min,Ju Xin,Shu Hang,Hu Cuiying,Li Liangzhi
β-Glucosidase (BG) hydrolyzes cellobiose into glucose, and is a vital step in converting ionic liquids (ILs)-pretreated biomass to sustainable biofuels. The inactivation mechanism of BG from Paenibacillus sp. LLZ1 induced by microcrystalline cellulose was explored in various concentrations of ILs, composed of [Emim] + cation and [DEP] − , [OAc] − , [Br] − , [Cl] − , and [BF 4 ] − anions. The FTIR analysis of inactivated BG indicated that the ILs altered its β-sheet content. Moreover, circular dichroism spectroscopy (CD) suggested that the α-helix content decreased, while the β-sheet content increased with the presence of ILs in general. Interestingly, the secondary structure of BG had almost no change after [Emim]DEP treatment, while ionic liquid [Emim]BF 4 treatment caused the irreversible denaturation of BG. Eventually, by adding 0.4 mM of Aerosol OT surfactant, the BG activity was increased by 20.1% in the presence of 25% [Emim]DEP, and the corresponding glucose yield from hydrolysis of cellobiose was increased by 23.9%.
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