SCIENCE OF THE TOTAL ENVIRONMENT
·
2021
·
IF 7.963
Zhengshi Chen,Haiyang Hu,Ping Xu,Hongzhi Tang
Polycyclic aromatic hydrocarbons (PAHs) commonly coexist in contaminated sites, posing a significant threat to ecosystem. Strains that degrade a wide range of substrates play important roles in bioremediation of contaminated environment. In this study, we reveal that Pseudomonas brassicacearum MPDS was able to remove 31.1% naphthalene of 500 mg/kg from soil within 2 d, while its relative abundance decreased significantly on Day 20, indicating its applicable potential in soil remediation . In addition to naphthalene, dibenzofuran , dibenzothiophene, and fluorene as reported previously, strain MPDS is able to degrade carbazole , phenanthrene , pyrene, and 2-bromonaphthalene. Moreover, NahA from strain MPDS has multi-substrate catalytic capacities on naphthalene, dibenzofuran, dibenzothiophene, phenanthrene, and 2-bromonaphthalene into dihydrodiols, while converts fluorene and carbazole into monohydroxy compounds according to GC–MS analysis. This study provides further insights into the exploration of soil remediation by strain MPDS and the mining of enzymes involved in the degradation of PAHs.
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Scientific Reports
·
2021
·Vol. 11
·期 1
·1-11
·
IF 4.38
Xue Shu-Wen,Tian Yue-Xin,Pan Jin-Cheng,Liu Ya-Ni,Ma Yan-Ling
Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His 217 -His 222 -Asp 372 for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C 7 -C 8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C 7 -O and C 8 -O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.
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ENVIRONMENTAL MICROBIOLOGY
·
2019
·Vol. 21
·期 5
·1847-1863
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IF 5.147
Lu Lin,Xiaopeng Wang,Lanfang Cao,Meiying Xu
Summary Lignin is one of the largest carbon reservoirs in the environment, playing an important role in the global carbon cycle. However, lignin degradation in bacteria, especially non-model organisms, has not been well characterized either enzymatically or genetically. Here, a lignin-degrading bacterial strain, Pseudomonas putida A514, was used as the research model. Genomic and proteomic analyses suggested that two B subfamily dye-decolorizing peroxidases (DypBs) were prominent in lignin depolymerization, while the classic O 2 -dependent ring cleavage strategy was utilized in central pathways to catabolize lignin-derived aromatic compounds that were funnelled by peripheral pathways. These enzymes, together with a range of transporters, sequential and expression-dose dependent regulation and stress response systems coordinated for lignin metabolism. Catalytic assays indicated these DypBs show unique Mn 2+ independent lignin depolymerization activity, while Mn 2+ oxidation activity is absent. Furthermore, a high synergy between DypB enzymes and A514 cells was observed to promote cell growth (5 × 10 12 cfus/ml) and lignin degradation (27%). This suggested DypBs are competitive lignin biocatalysts and pinpointed limited extracellular secretion capacity as the rate-limiting factor in bacterial lignin degradation. DypB production was, therefore, optimized in recombinant strains and a 14,141-fold increase in DypB activity (56,565 U/l) was achieved, providing novel insights for lignin bioconversion.
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MOLECULES
·
2015
·Vol. 20
·期 9
·16266-16277
·
IF 2.416
Zaixiang Lou,Yuxia Tang,Xinyi Song,Hongxin Wang
Screening of anti-biofilm compounds from the burdock leaf based on metabolomics is reported here. The crystal violet assay indicated 34% ethanol elution fraction of burdock leaf could completely inhibit biofilm formation ofPseudomonas aeruginosaat 1 mg·mL−1. Then, the chemical composition of burdock leaf fraction was analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and 11 active compounds (chlorogenic acid, caffeic acid,p-coumaric acid, quercetin, ursolic acid, rutin, cynarin, luteolin, crocin, benzoic acid, and Tenacissoside I) were identified. Lastly, UPLC-MS analysis was employed to obtain the metabolic fingerprints of burdock leaf fractions before and after inhibiting the biofilm ofPseudomonas aeruginosa. The metabolic fingerprints were transformed to data, analyzed with PLS-DA (partial least squares discriminant analysis) and the peaks whose area was significantly changed were found out. Thus, 81 compounds were screened as potential anti-biofilm ingredients. Among them, rutin, ursolic acid, caffeic acid,p-coumaric acid and quercetin were identified and confirmed as the main anti-biofilm compounds in burdock leaf. The study provided basic anti-biofilm profile data for the compounds in burdock leaf, as well as provided a convenient method for fast screening of anti-biofilm compounds from natural plants.Keywords:screening;anti-biofilm compounds;burdock leaf;metabolomics;data analysis
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BIORESOURCE TECHNOLOGY
·
2017
·
IF 5.651
Qian Chen,Tingting Li,Mengyao Gui,Shufeng Liu,Maosheng Zheng,Jinren Ni
Anaerobic denitrification has been proved to be negatively affected by ZnO nanomaterials (NPs), but little is known about how ZnO NPs affects aerobic denitrification. In this study, inhibition of ZnO NPs to an aerobic denitrifier, Pseudomonas stutzeri PCN-1, was firstly reported. The results showed total nitrogen removal efficiency was decreased from 100% to 1.70% with the increase of ZnO NPs from 1 to 128 mg/L. The presence of ZnO NPs caused significant inhibition of gene expressions and catalytic activities of nitrate reductase and nitrite reductase, which finally led to delayed nitrate reduction and high nitrite accumulation. Further studies revealed that the deposition of nanoparticles on the bacterial surface caused by electrostatic forces and the generation of reactive oxygen species (ROS) were responsible for the cytotoxicity of ZnO NPs, where ROS played a more important role. These results were of significance to evaluating the potential ecological toxicity and risks of nanomaterials.
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Journal of Extracellular Vesicles
·
2024
·Vol. 13
·期 10
·e12524
·
IF 15.5
Xinran Peng,Yuanjing Luo,Li Yang,Yi Yan Yang,Peiyan Yuan,Xinhai Chen,Guo-Bao Tian,Xin Ding
Bacterial infections, especially those caused by multidrug-resistant pathogens, pose a significant threat to public health. Vaccines are a crucial tool in fighting these infections; however, no clinically available vaccine exists for the most common bacterial infections, such as those caused by Pseudomonas aeruginosa . Herein, a multiantigenic antibacterial nanovaccine (AuNP@HMV@SPs) is reported to combat P. aeruginosa infections. This nanovaccine utilizes the hybrid membrane vesicles (HMVs) created by fusing macrophage membrane vesicles (MMVs) with bacterial outer membrane vesicles (OMVs). The HMVs mitigate the toxic effects of both OMVs and bacterial secreted toxins (SP) adsorbed on the surface of MMVs, while preserving their stimulating properties. Gold nanoparticles (AuNPs) are utilized as adjuvant to enhance immune response without comprising safety. The nanovaccine AuNP@HMV@SPs induces robust humoral and cellular immune responses, leading to destruction of bacterial cells and neutralization of their secreted toxins. In murine models of septicemia and pneumonia caused by P. aeruginosa , AuNP@HMV@SPs exhibits superior prophylactic efficacy compared to control groups including OMVs, or MMVs@SPs and HMV@SPs, achieving 100% survival in septicemia and > 99.9% reduction in lung bacterial load in pneumonia. This study highlights AuNP@HMV@SPs as a safe and effective antibacterial nanovaccine, targeting both bacteria and their secreted toxins, and offers a promising platform for developing multiantigenic antibacterial vaccines against multidrug-resistant pathogens.
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BIOCHEMICAL ENGINEERING JOURNAL
·
2024
·
IF 3.7
Zhimei Zhang,Chao Zhao,Tianming Wu,Yanfeng Xu,Lu Wang,Yusheng Niu
The accumulation of glyphosate during its application in agriculture and its toxicity seriously threaten ecosystems and human health. Currently, glyphosate residual contamination is mainly accomplished through bioremediation techniques based on enhanced microbial degradation activity. However, there are drawbacks, such as poor environmental adaptability of strains and low degradation efficiency. Therefore, in this study, an efficient glyphosate-degrading strain, Pseudomonas alcaligenes Z1–1, was isolated from herbicide-contaminated environments and was capable of completely degrading glyphosate at a concentration of 200 mg/L within 7 days. Kinetics analysis showed that glyphosate degradation was concentration-dependent, with a maximum tolerant concentration of 800 mg/L. Mass spectrometric analysis indicated that AminoMethylPhosphonic acid (AMPA) was the predominant intermediate produced in the degradation pathway of glyphosate, revealing that glyphosate destruction began with breaking the C-N bond. Whole genome sequencing identified the key genes potentially involved in glyphosate degradation, including the thiO , glpA , aroA , soxB , and argA genes. Furthermore, in contrast to the majority of the metabolic pathways previously reported for glyphosate degradation via glyphosate oxidoreductase , the breaking of the C-N bond was primarily catalyzed by glycine oxidase . Overall, this research provides novel insights into the mechanisms of glyphosate degradation, offering valuable degradation enzyme resources for future applications.
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Communications Biology
·
2025
·Vol. 8
·期 1
·1-13
·
IF 5.1
Liang Congying,Lin Lu,Wang Xiaoyan,Zhu Wenping
The secretion of ligninolytic enzyme provides a competitive advantage for microbial survival. These enzymes are commonly transported to the extracellular milieu via signal peptides for the catabolism of lignin, which cannot be translocated through the cell membrane. However, some bacterial ligninolytic enzymes lack signal peptides, yet they can still be secreted. It remains unclear how these unconventional proteins cross the cell membrane. Here, we reveal a secretion mechanism for the unconventional B-type dye-decolorizing peroxidase (DypB) in Pseudomonas putida A514. Type VI secretion system (T6SS) mediates the inner membrane channel, where interaction of DypB with the T6SS components VgrG and Hcp accounts for periplasmic delivery. Once in the periplasm, DypB is allocated into outer membrane vesicles (OMVs) and released to the extracellular space. The crosslinked translocation model for DypB delivery represents an ingenious mechanism by which bacteria harness extant systems to thrive in a nutrient-poor environment. Moreover, we develop an OMV-surface display platform to improve DypB secretion and further enhance lignin utilization, exemplifying the applicability of OMVs as a lignin biocatalytic nanoreactor. Our study demonstrates the previously unrecognized crosslinking of T6SS and OMVs for the secretion of unconventional ligninolytic peroxidase and provides new perspectives on its biotechnological applications.
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JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE
·
2018
·Vol. 55
·期 8
·3016-3025
·
IF 1.797
Li Tingting,Yang Bing,Li Xuepeng,Li Jianrong,Zhao Guohua,Kan Jianquan
The spoilage of aquatic products is mainly caused by the bacterial growth, and the specific spoilage organism (SSO) plays an important role. Quorum sensing (QS) is a microbial cell–cell communication system which is coordinated with the population density, and is controlled by N -acyl-homoserine lactone (AHLs) as the Gram-negative bacteria communication signals. In this study, the SSO was Pseudomonas fluorescens (PF-04), isolated from the turbot ( Scophthalmus maximus L. ) during aerobically refrigerated storage. The supernatant extract of PF-04 tested the AHLs activities utilizing biosensor Chromobacterium violaceum CV026. AHL production was influenced by the environment temperature, and AHL production reduced obviously at 10 °C compare with 25 °C. In Luria-Bertani (LB) supplemented with 0.5–1.0% NaCl, AHL production reached the maximum. The AHL production was also regulated by pH of culture medium, acidic condition was conducive to persistent existence of the AHL molecules, but the alkaline environment would cause chemically unstable of AHL molecules. QS system in P. flurosecens played an imperative role in biofilm formation, protease and siderophore production. AHLs could regulate above three factors in PF-04. In summary, this study showed that (1) the influence of different environmental conditions (temperature, NaCl and pH) on AHL production revealed the correlation of QS in foods and (2) that proved the effect of external AHLs to regulate the biofilm formation, protease and siderophore production in PF-04.
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BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY
·
2016
·Vol. 97
·期 5
·689-694
·
IF 1.191
Jin Jingnan,Yao Jun,Zhang Qingye
The strain Pseudomonas sp. JPN2 had a high potential to degrade phenanthrene degrading 98.52 % of the initial amount of 100 mg L −1 after 10 days incubation. The analysis of metabolites demonstrated that the cleavage of phenanthrene started at the C 9 and C 10 positions on the aromatic ring by the dioxygenation reaction, and then further degraded via a phthalate pathway. To understand the interaction between phenanthrene and the amino acid residues in the active site of the target enzyme, a molecular docking simulation was performed. The results showed that the distances of C 9 –O 1 and C 10 –O 2 atoms were 3.47 and 3.67 Å, respectively. The C 9 and C 10 positions of the phenanthrene ring are much closer to the dioxygen molecule in the active site relative to the other atoms. Therefore, the C 9 and C 10 positions are vulnerable to attack in the initial oxygenation process.
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WATER RESEARCH
·
2017
·
IF 6.942
Yuancai Lv,Zhuyu Niu,Yuancai Chen,Yongyou Hu
With the introduction of nano zero valent iron (nZVI) technology into our environment, its potential environmental risk to environmental microorganisms has attracted considerable attention. In this study, Pseudomonas putida was chosen as a typical strain to study the bacterial toxicity of nZVI/Pd. The CFU assay results indicated that nZVI/Pd was toxic to P. putida cells but the toxicity decreased with an increase in DO. The experiments isolated by dialysis bag and flow cytometry analysis suggested that both membrane disruption caused by direct contact and oxidative stress were the main bactericidal mechanisms under the aerobic condition , while membrane disruption resulting from direct contact was the primary bactericidal mechanism in the anaerobic system. Furthermore, according to TEM, SEM, EDS , XRD , FTIR and XPS , it was indicated that in the aerobic system, the reactive oxygen species (ROS) generated by nZVI/Pd could oxidize the amide and hydroxyl groups into carboxyl groups , resulting in a decline in peptides and increase in polysaccharides . In addition, the ROS also accumulated inside the cell and caused cell inactivation via oxidative stress . In the anaerobic system, the adhered nZVI/Pd particles would attack the functional groups such as carboxyl, ester and amide, leading to the decline in proteins and polysaccharides and subsequent damage of the membrane. The findings provide a significant guide for the application of nano-bio combined technology.
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Food Bioscience
·
2024
·
IF 4.8
Dangfeng Wang,Benyou Zhang,Yunting Wang,Likun Ren,Yuqiong Meng,Rui Ma,Shulin Wang,Zhiteng Liu,Yang Jiang,Fangchao Cui,Tingting Li,Jianrong Li
LuxR solos sense exogenous signaling molecules and regulate microbial behaviors, thus facilitating intra- and inter-species communication among bacteria. However, studies on the role of LuxR solos in regulating the spoilage potential of specific spoilage organisms are limited. In this study, we screened a LuxR solo EvgA, derived from Pseudomonas fluorescens PF08. qRT-PCR and molecular docking results indicated that EvgA responds and binds most strongly to exogenous N -3-tetradecanoyl-L-homoserine lactone (C14-HSL) through hydrogen bonds and hydrophobic interactions, with a –CDOCKER ENERGY of 45.87 kcal/mol. Subsequently, the evgA knockout (Δ evgA ) and complementary evgA (Δ evgA -com) mutants of P. fluorescens PF08 were constructed through homologous recombination. Δ evgA mutants displayed diminished eavesdropping to exogenous C14-HSL (by 18.99 ± 2.09%), reduced adhesion ability (by 30.33 ± 0.36%), attenuated biofilm formation (by 15.97 ± 0.14%), and decreased motility (swarming zones by 4.34 ± 0.002 mm and swimming zones by 4.17 ± 0.11 mm). In addition, EvgA deletion reduced spoilage factor production (hydrolysis zone), which included extracellular proteases, lipases, and biogenic amines (by 4.45 ± 0.51 mm, 10.12 ± 0.10 mm, and 14.41 ± 0.57 mm, respectively), thereby diminishing the spoilage of salmon fillets stored at 4 °C. Notably, the addition of exogenous C14-HSL promoted the spoilage ability of all strains. This study emphasizes the important role of LuxR solo EvgA in AHLs-mediated quorum sensing and the spoilage potential of P. fluorescens PF08, which is expected to be a new target for controlling the spoilage of aquatic products.
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