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Miura D, Tsurigami R, Kato H, Wariishi H, Shimizu M. Pathway crosstalk between the central metabolic and heme biosynthetic pathways in Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2024; 108:37. [PMID: 38183476 PMCID: PMC10771590 DOI: 10.1007/s00253-023-12846-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 01/08/2024]
Abstract
A comprehensive analysis to survey heme-binding proteins produced by the white-rot fungus Phanerochaete chrysosporium was achieved using a biotinylated heme-streptavidin beads system. Mitochondrial citrate synthase (PcCS), glyceraldehyde 3-phosphate dehydrogenase (PcGAPDH), and 2-Cys thioredoxin peroxidase (mammalian HBP23 homolog) were identified as putative heme-binding proteins. Among these, PcCS and PcGAPDH were further characterized using heterologously expressed recombinant proteins. Difference spectra of PcCS titrated with hemin exhibited an increase in the Soret absorbance at 414 nm, suggesting that the axial ligand of the heme is a His residue. The activity of PcCS was strongly inhibited by hemin with Ki oxaloacetate of 8.7 μM and Ki acetyl-CoA of 5.8 μM. Since the final step of heme biosynthesis occurred at the mitochondrial inner membrane, the inhibition of PcCS by heme is thought to be a physiological event. The inhibitory mode of the heme was similar to that of CoA analogues, suggesting that heme binds to PcCS at His347 at the AcCoA-CoA binding site, which was supported by the homology model of PcCS. PcGAPDH was also inhibited by heme, with a lower concentration than that for PcCS. This might be caused by the different location of these enzymes. From the integration of these phenomena, it was concluded that metabolic regulations by heme in the central metabolic and heme synthetic pathways occurred in the mitochondria and cytosol. This novel pathway crosstalk between the central metabolic and heme biosynthetic pathways, via a heme molecule, is important in regulating the metabolic balance (heme synthesis, ATP synthesis, flux balance of the tricarboxylic acid (TCA) cycle and cellular redox balance (NADPH production) during fungal aromatic degradation. KEY POINTS: • A comprehensive survey of heme-binding proteins in P. chrysosporium was achieved. • Several heme-binding proteins including CS and GAPDH were identified. • A novel metabolic regulation by heme in the central metabolic pathways was found.
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Affiliation(s)
- Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
| | - Ryoga Tsurigami
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Kato
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Wariishi
- Faculty of Arts and Science, Kyushu University, Fukuoka, Fukuoka, 819-0395, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan.
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Zhao S, Shi R, Liang X, Li P, Bai X, Wang Y, Zhang Y. Sulfadiazine degradation by Bjerkandera adusta DH0817 at low temperatures and its cold-adaptation mechanisms. BIORESOURCE TECHNOLOGY 2024; 407:131108. [PMID: 39009046 DOI: 10.1016/j.biortech.2024.131108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/29/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]
Abstract
The prolonged period of low temperatures in northern China poses a significant challenge to the bioremediation of antibiotic pollution. This study reports that a white-rot fungus Bjerkandera adusta DH0817, isolated from a poultry farm in Liaoning Province, can remove 60 % of SDZ within 20 days at 10°C and reduce the biotoxicity of SDZ. Six degradation pathways were proposed. SDZ biodegradation was primarily driven by cytochrome P450. Transcriptome analysis revealed that DH0817 upregulated genes associated with cell membrane, transcription factors and soluble sugars in response to low temperatures. Subsequently, genes associated with fatty acid, proteins and enzymes were upregulated to remove SDZ at low temperatures. This study provides valuable microbial resources and serves as a theoretical reference for addressing antibiotic pollution in livestock and poultry farms under low temperature conditions.
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Affiliation(s)
- Shuang Zhao
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongjiu Shi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xiaolong Liang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Ping Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Bai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongfeng Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Ying Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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Zhang LB, Qiu XG, Qiu TT, Cui Z, Zheng Y, Meng C. A complex metabolic network and its biomarkers regulate laccase production in white-rot fungus Cerrena unicolor 87613. Microb Cell Fact 2024; 23:167. [PMID: 38849849 PMCID: PMC11162070 DOI: 10.1186/s12934-024-02443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND White-rot fungi are known to naturally produce high quantities of laccase, which exhibit commendable stability and catalytic efficiency. However, their laccase production does not meet the demands for industrial-scale applications. To address this limitation, it is crucial to optimize the conditions for laccase production. However, the regulatory mechanisms underlying different conditions remain unclear. This knowledge gap hinders the cost-effective application of laccases. RESULTS In this study, we utilized transcriptomic and metabolomic data to investigate a promising laccase producer, Cerrena unicolor 87613, cultivated with fructose as the carbon source. Our comprehensive analysis of differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) aimed to identify changes in cellular processes that could affect laccase production. As a result, we discovered a complex metabolic network primarily involving carbon metabolism and amino acid metabolism, which exhibited contrasting changes between transcription and metabolic patterns. Within this network, we identified five biomarkers, including succinate, serine, methionine, glutamate and reduced glutathione, that played crucial roles in co-determining laccase production levels. CONCLUSIONS Our study proposed a complex metabolic network and identified key biomarkers that determine the production level of laccase in the commercially promising Cerrena unicolor 87613. These findings not only shed light on the regulatory mechanisms of carbon sources in laccase production, but also provide a theoretical foundation for enhancing laccase production through strategic reprogramming of metabolic pathways, especially related to the citrate cycle and specific amino acid metabolism.
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Affiliation(s)
- Long-Bin Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, China.
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, 350108, China.
| | - Xiu-Gen Qiu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, China
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Ting-Ting Qiu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, China
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Zhou Cui
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yan Zheng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Chun Meng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, China.
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, 350108, China.
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Akrout I, Staita K, Zouari-Mechichi H, Ghariani B, Khmaissa M, Navarro D, Doan A, Albert Q, Faulds C, Sciara G, Record E, Mechichi T. Valorizing fungal diversity for the degradation of fluoroquinolones. Heliyon 2024; 10:e30611. [PMID: 38799738 PMCID: PMC11126791 DOI: 10.1016/j.heliyon.2024.e30611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Continued widespread use of antibiotics, especially fluoroquinolones, raises environmental concerns, as its driving bacterial resistance and disrupts microbial ecosystems. Here we investigate the biodegradation of ten fluoroquinolone antibiotics (six for medical use and four for veterinary use) by ligninolytic fungi, including Trametes versicolor, Bjerkandera adusta, Porosterum spadiceum, Irpex lacteus, Pleuroteus ostreatus, Phanerochaete chrysosporium, Pycnoporus cinnabarinus, Ganoderma lucidum, and Gloeophyllum trabeum. The results show significant variations between strains in the efficiency of antibiotic transformation. B. adusta and P. spadiceum were the fungi that most efficiently reduced antibiotic concentrations and were able to totally degrade eight and six antibiotics, respectively, within a 15-day period. T. versicolor and P. ostreatus also showed the ability to effectively degrade antibiotics. Specifically, T. versicolor degraded six out of the ten fluoroquinolone antibiotics by more than 70 %, while P. ostreatus degraded the tested antibiotics between 43 % and 100 %. The remaining antibiotic activity did not always correlate with a reduction in antibiotic concentrations, which points to the presence of post-transformation antimicrobial metabolites. This study also explores the potential mechanisms used by these fungi to remove selected models of fluroquinolones via enzymatic routes, such as oxidation by laccases, heme-peroxidases, and cytochrome P450, or via adsorption on fungal biomass.
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Affiliation(s)
- Imen Akrout
- Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, Laboratoire de Biochimie et de Génie Enzymatique des Lipases, 3038 Sfax, Tunisia
- Aix-Marseille Université, INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Karima Staita
- Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, Laboratoire de Biochimie et de Génie Enzymatique des Lipases, 3038 Sfax, Tunisia
- Aix-Marseille Université, INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Hèla Zouari-Mechichi
- Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, Laboratoire de Biochimie et de Génie Enzymatique des Lipases, 3038 Sfax, Tunisia
| | - Bouthaina Ghariani
- Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, Laboratoire de Biochimie et de Génie Enzymatique des Lipases, 3038 Sfax, Tunisia
| | - Marwa Khmaissa
- Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, Laboratoire de Biochimie et de Génie Enzymatique des Lipases, 3038 Sfax, Tunisia
| | - David Navarro
- Aix-Marseille Université, INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Annick Doan
- Aix-Marseille Université, INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Quentin Albert
- Aix-Marseille Université, INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Craig Faulds
- Aix-Marseille Université, INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Giuliano Sciara
- Aix-Marseille Université, INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Eric Record
- Aix-Marseille Université, INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Tahar Mechichi
- Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, Laboratoire de Biochimie et de Génie Enzymatique des Lipases, 3038 Sfax, Tunisia
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Kong W, Zhang X, Fu X, Zhou C, Fan L, Zhang W. Biological pretreatment with white rot fungi for preparing hierarchical porous carbon from Banlangen residues with high performance for supercapacitors and dye adsorption. Front Microbiol 2024; 15:1374974. [PMID: 38873140 PMCID: PMC11169573 DOI: 10.3389/fmicb.2024.1374974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
White rot fungi possess superior infiltrability and biodegradability on lignocellulosic substrates, allowing them to form tailored microstructures which are conducive to efficient carbonization and chemical activation. The present research employed white rot fungus pretreatment as a viable approach for preparing porous carbon from Banlangen residues. The resultant F-A-BLGR-PC prepared by pretreating Banlangen residues with white rot fungi followed by carbonization and activation has a hierarchical porous structure with a high specific surface area of 898 m2 g-1, which is 43.4% greater than that of the unprocessed sample (R-BLGR-PC). When used as an electrode for supercapacitors, the F-A-BLGR-PC demonstrated a high specific capacitance of 308 F g-1 at 0.5 A g-1 in 6 M KOH electrolyte in three-electrode configuration. Moreover, the F-A-BLGR-PC based symmetric supercapacitor device achieved a superb cyclic stability with no obvious capacitance decay after 20,000 cycles at 5 A g-1 in 1 M Na2SO4 electrolyte. Additionally, the F-A-BLGR-PC sample was found to be an ideal adsorbent for removing methyl orange (MO) from water, exhibiting an adsorption ability of 173.4 mg g-1 and a maximum removal rate of 86.6%. This study offers a promising method for the preparation of a porous carbon with a high specific surface area in a biological way using white rot fungi pretreatment, and the derived carbon can not only be applied in energy storage but also in environmental remediation, catalysis, and so on.
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Affiliation(s)
| | | | | | | | | | - Wanju Zhang
- Hubei Key Lab for Processing and Application of Catalytic Materials, LiShizhen College of Traditional Chinese Medicine, Huanggang Normal University, Huanggang, China
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Abd El-Latif AS, Zohri ANA, El-Aref HM, Mahmoud GAE. Kinetic studies on optimized extracellular laccase from Trichoderma harzianum PP389612 and its capabilities for azo dye removal. Microb Cell Fact 2024; 23:150. [PMID: 38790055 PMCID: PMC11127416 DOI: 10.1186/s12934-024-02412-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Azo dyes represent a common textile dye preferred for its high stability on fabrics in various harsh conditions. Although these dyes pose high-risk levels for all biological forms, fungal laccase is known as a green catalyst for its ability to oxidize numerous dyes. METHODS Trichoderma isolates were identified and tested for laccase production. Laccase production was optimized using Plackett-Burman Design. Laccase molecular weight and the kinetic properties of the enzyme, including Km and Vmax, pH, temperature, and ionic strength, were detected. Azo dye removal efficiency by laccase enzyme was detected for Congo red, methylene blue, and methyl orange. RESULTS Eight out of nine Trichoderma isolates were laccase producers. Laccase production efficiency was optimized by the superior strain T. harzianum PP389612, increasing production from 1.6 to 2.89 U/ml. In SDS-PAGE, purified laccases appear as a single protein band with a molecular weight of 41.00 kDa. Km and Vmax values were 146.12 μmol guaiacol and 3.82 μmol guaiacol/min. Its activity was stable in the pH range of 5-7, with an optimum temperature range of 40 to 50 °C, optimum ionic strength of 50 mM NaCl, and thermostability properties up to 90 °C. The decolorization efficiency of laccase was increased by increasing the time and reached its maximum after 72 h. The highest efficiency was achieved in Congo red decolorization, which reached 99% after 72 h, followed by methylene blue at 72%, while methyl orange decolorization efficiency was 68.5%. CONCLUSION Trichoderma laccase can be used as an effective natural bio-agent for dye removal because it is stable and removes colors very well.
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Affiliation(s)
| | - Abdel-Naser A Zohri
- Botany and Microbiology Department, Faculty of Science, Assiut University, P.O. 71516, Assiut, Egypt
| | - Hamdy M El-Aref
- Genetics Department, Faculty of Agriculture, Assiut University, Assiut, Egypt
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Chen X, Zhu Y, Zheng W, Yan S, Li Y, Xie S. Elucidating doxycycline biotransformation mechanism by Chryseobacterium sp. WX1: Multi-omics insights. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133975. [PMID: 38452667 DOI: 10.1016/j.jhazmat.2024.133975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Doxycycline (DOX) represents a second-generation tetracycline antibiotic that persists as a challenging-to-degrade contaminant in environmental compartments. Despite its ubiquity, scant literature exists on bacteria proficient in DOX degradation. This study marked a substantial advancement in this field by isolating Chryseobacterium sp. WX1 from an activated sludge enrichment culture, showcasing its unprecedented ability to completely degrade 50 mg/L of DOX within 44 h. Throughout the degradation process, seven biotransformation products were identified, revealing a complex pathway that began with the hydroxylation of DOX, followed by a series of transformations. Employing an integrated multi-omics approach alongside in vitro heterologous expression assays, our study distinctly identified the tetX gene as a critical facilitator of DOX hydroxylation. Proteomic analyses further pinpointed the enzymes postulated to mediate the downstream modifications of DOX hydroxylation derivatives. The elucidated degradation pathway encompassed several key biological processes, such as the microbial transmembrane transport of DOX and its intermediates, the orchestration of enzyme synthesis for transformation, energy metabolism, and other gene-regulated biological directives. This study provides the first insight into the adaptive biotransformation strategies of Chryseobacterium under DOX-induced stress, highlighting the potential applications of this strain to augment DOX removal in wastewater treatment systems containing high concentrations of DOX.
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Affiliation(s)
- Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Wenli Zheng
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yangyang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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8
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Cao S, Duan M, Zhang X, Yang Z, Zhuo R. Bacterial community structure analysis of sludge from Taozi lake and isolation of an efficient 17β-Estradiol (E2) degrading strain Sphingobacterium sp. GEMB-CSS-01. CHEMOSPHERE 2024; 355:141806. [PMID: 38548087 DOI: 10.1016/j.chemosphere.2024.141806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/28/2024] [Accepted: 03/24/2024] [Indexed: 04/08/2024]
Abstract
Environmental challenges arising from organic pollutants pose a significant problem for modern societies. Efficient microbial resources for the degradation of these pollutants are highly valuable. In this study, the bacterial community structure of sludge samples from Taozi Lake (polluted by urban sewage) was studied using 16S rRNA sequencing. The bacterial phyla Proteobacteria, Bacteroidetes, and Chloroflexi, which are potentially important in organic matter degradation by previous studies, were identified as the predominant phyla in our samples, with relative abundances of 48.5%, 8.3%, and 6.6%, respectively. Additionally, the FAPROTAX and co-occurrence network analysis suggested that the core microbial populations in the samples may be closely associated with organic matter metabolism. Subsequently, sludge samples from Taozi Lake were subjected to enrichment cultivation to isolate organic pollutant-degrading microorganisms. The strain Sphingobacterium sp. GEMB-CSS-01, tolerant to sulfanilamide, was successfully isolated. Subsequent investigations demonstrated that Sphingobacterium sp. GEMB-CSS-01 efficiently degraded the endocrine-disrupting compound 17β-Estradiol (E2). It achieved degradation efficiencies of 80.0% and 53.5% for E2 concentrations of 10 mg/L and 20 mg/L, respectively, within 10 days. Notably, despite a reduction in degradation efficiency, Sphingobacterium sp. GEMB-CSS-01 retained its ability to degrade E2 even in the presence of sulfanilamide concentrations ranging from 50 to 200 mg/L. The findings of this research identify potential microbial resources for environmental bioremediation, and concurrently provide valuable information about the microbial community structure and patterns within Taozi Lake.
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Affiliation(s)
- Shanshan Cao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China; Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China
| | - Mifang Duan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Xuan Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, 410004, PR China
| | - Zhilong Yang
- Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China
| | - Rui Zhuo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China; Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China.
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9
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Hu M, Scott C. Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances. Appl Environ Microbiol 2024; 90:e0015724. [PMID: 38477530 PMCID: PMC11022551 DOI: 10.1128/aem.00157-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
Per- and polyfluoroalkyl substances (PFAS) are highly fluorinated synthetic organic compounds that have been used extensively in various industries owing to their unique properties. The PFAS family encompasses diverse classes, with only a fraction being commercially relevant. These substances are found in the environment, including in water sources, soil, and wildlife, leading to human exposure and fueling concerns about potential human health impacts. Although PFAS degradation is challenging, biodegradation offers a promising, eco-friendly solution. Biodegradation has been effective for a variety of organic contaminants but is yet to be successful for PFAS due to a paucity of identified microbial species capable of transforming these compounds. Recent studies have investigated PFAS biotransformation and fluoride release; however, the number of specific microorganisms and enzymes with demonstrable activity with PFAS remains limited. This review discusses enzymes that could be used in PFAS metabolism, including haloacid dehalogenases, reductive dehalogenases, cytochromes P450, alkane and butane monooxygenases, peroxidases, laccases, desulfonases, and the mechanisms of microbial resistance to intracellular fluoride. Finally, we emphasize the potential of enzyme and microbial engineering to advance PFAS degradation strategies and provide insights for future research in this field.
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Affiliation(s)
- Miao Hu
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Colin Scott
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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10
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Alhujaily A, Mawad AMM, Albasri HM, Fuying M. Efficiency of thermostable purified laccase isolated from Physisporinus vitreus for azo dyes decolorization. World J Microbiol Biotechnol 2024; 40:138. [PMID: 38509412 DOI: 10.1007/s11274-024-03953-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
Laccases are versatile biocatalysts that are prominent for industrial purposes due to their extensive substrate specificity. Therefore, this research investigated producing laccase from Physisporinus vitreus via liquid fermentation. The results revealed that veratryl alcohol (4mM) was the most effective inducer 7500U/L. On the other hand, Zn ions inhibited laccase production. The optimum carbon and nitrogen sources were glucose and tryptone by 5200 and 3300 U/L, respectively. Moreover, solvents exhibited various impacts on the enzyme activity at three different solvent concentrations (5%, 10% and 20%), however, it showed a highest activity at 5% of the investigated solvent. Ferric ions inhibited the enzyme activity. In addition, the enzyme has a high ability to decolorize azo dyes when using syringaldehyde as a mediator. The purified laccase from Physisporinus vitreus is a promising substance to be used for industrial and environmental applications due to its stability under harsh conditions and efficiency in decolorization of dyes.
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Affiliation(s)
- Ahmad Alhujaily
- Department of Biology, College of Science, Taibah University, Madinah, 30001, Saudi Arabia.
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China.
| | - Asmaa M M Mawad
- Department of Biology, College of Science, Taibah University, Madinah, 30001, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, 71516, Egypt
| | - Hibah M Albasri
- Department of Biology, College of Science, Taibah University, Madinah, 30001, Saudi Arabia
| | - Ma Fuying
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China.
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11
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Changotra R, Rajput H, Liu B, Murray G, He QS. Occurrence, fate, and potential impacts of wood preservatives in the environment: Challenges and environmentally friendly solutions. CHEMOSPHERE 2024; 352:141291. [PMID: 38280646 DOI: 10.1016/j.chemosphere.2024.141291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 01/29/2024]
Abstract
Wood preservation has gained global prevalence in recent years, primarily owing to the renewable nature of wood and its capacity to act as a carbon sink. Wood, in its natural form, lacks intrinsic resilience and is prone to decay if left untreated; hence, wood preservatives (WPs) are used to improve wood's longevity. The fate and potential hazards of wood preservatives to human health, ecosystems, and the environment are complex and depend on various aspects, including the type of the preservative compounds, their physicochemical properties, application methods, exposure pathways, environmental conditions, and safety measures and guidelines. The occurrence and distribution of WPs in environmental matrices such as soil and water can result in hazardous pollutants seeping into surface water, groundwater, and soil, posing health hazards, and polluting the environment. Bioremediation is crucial to safeguarding the environment and effectively removing contaminants through hydrolytic and/or photochemical reactions. Phytoremediation, vermicomposting, and sustainable adsorption have demonstrated significant efficacy in the remediation of WPs in the natural environment. Adsorbents derived from biomass waste have been acknowledged for their ability to effectively remove WPs, while also offering cost-efficiency and environmental sustainability. This paper aims to identify wood preservatives' sources and fate in the environment and present a comprehensive overview of the latest advancements in environmentally friendly methods relevant to the removal of the commonly observed contaminants associated with WPs in environmental matrices.
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Affiliation(s)
- Rahil Changotra
- Department of Engineering, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Himadri Rajput
- Department of Engineering, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Baoshu Liu
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, China
| | - Gordon Murray
- Stella-Jones Inc. Truro, Nova Scotia, B2N 5C1, Canada
| | - Quan Sophia He
- Department of Engineering, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada.
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Gao X, Wei M, Zhang X, Xun Y, Duan M, Yang Z, Zhu M, Zhu Y, Zhuo R. Copper removal from aqueous solutions by white rot fungus Pleurotus ostreatus GEMB-PO1 and its potential in co-remediation of copper and organic pollutants. BIORESOURCE TECHNOLOGY 2024; 395:130337. [PMID: 38244937 DOI: 10.1016/j.biortech.2024.130337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
Addressing the environmental contamination from heavy metals and organic pollutants remains a critical challenge. This study explored the resilience and removal potential of Pleurotus ostreatus GEMB-PO1 for copper. P. ostreatus GEMB-PO1 showed significant tolerance, withstanding copper concentrations up to 2 mM. Its copper removal efficiency ranged from 64.56 % at 0.5 mM to 22.90 % at 8 mM. Transcriptomic insights into its response to copper revealed a marked upregulation in xenobiotic degradation-related enzymes, such as laccase and type II peroxidases. Building on these findings, a co-remediation system using P. ostreatus GEMB-PO1 was developed to remove both copper and organic pollutants. While this approach significantly enhanced the degradation efficiency of organic contaminants, it concurrently exhibited a diminished efficacy in copper removal within the composite system. This study underscores the potential of P. ostreatus GEMB-PO1 in environmental remediation. Nevertheless, further investigation is required to optimize the simultaneous removal of organic pollutants and copper.
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Affiliation(s)
- Xuan Gao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China; Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang 422000, PR China
| | - Mi Wei
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Xiaodan Zhang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China
| | - Yu Xun
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China
| | - Mifang Duan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China
| | - Zhilong Yang
- Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang 422000, PR China
| | - Mingdong Zhu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China
| | - Yonghua Zhu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China
| | - Rui Zhuo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China; Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang 422000, PR China.
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13
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Liu Y, Chen Y, Zhang J, Ran G, Cheng Z, Wang X, Liao Y, Mao X, Peng Y, Li W, Zheng J. Dihydrotanshinone I-Induced CYP1 Enzyme Inhibition and Alteration of Estradiol Metabolism. Drug Metab Dispos 2024; 52:188-197. [PMID: 38123940 DOI: 10.1124/dmd.123.001490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Dihydrotanshinone I (DHTI) is a pharmacologically active component occurring in the roots of the herbal medicine Salvia miltiorrhiza Bunge. This study investigated DHTI-induced inhibition of CYP1A1, CYP1A2, and CYP1B1 with the aim to determine the potential effects of DHTI on the bioactivation of estradiol (E2), possibly related to preventive/therapeutic strategy for E2-associated breast cancer. Ethoxyresorufin as a specific substrate for CYP1s was incubated with human recombinant CYP1A1, CYP1A2, or CYP1B1 in the presence of DHTI at various concentrations. Enzymatic inhibition and kinetic behaviors were examined by monitoring the formation of the corresponding product. Molecular docking was further conducted to define the interactions between DHTI and the three CYP1s. The same method and procedure were employed to examine the DHTI-induced alteration of E2 metabolism. DHTI showed significant inhibition of ethoxyresorufin O-deethylation activity catalyzed by CYP1A1, CYP1A2 and CYP1B1 in a concentration-dependent manner (IC50 = 0.56, 0.44, and 0.11 μM, respectively). Kinetic analysis showed that DHTI acted as a competitive type of inhibitor of CYP1A1 and CYP1B1, whereas it noncompetitively inhibited CYP1A2. The observed enzyme inhibition was independent of NADPH and time. Molecular docking analysis revealed hydrogen bonding interactions between DHTI and Asp-326 of CYP1B1. Moreover, DHTI displayed preferential activity to inhibit 4-hydroxylation of E2 (a genotoxic pathway) mediated by CYP1B1. Exposure to DHTI could reduce the risk of genotoxicity induced by E2. SIGNIFICANCE STATEMENT: CYP1A1, CYP1A2, and CYP1B1 enzymes are involved in the conversion of estradiol (E2) into 2-hydroxyestradiol (2-OHE2) and 4-hydroxyestradiol (4-OHE2) through oxidation. 2-OHE2 is negatively correlated with breast cancer risk, and 4-OHE2 may be a significant initiator and promoter of breast cancer. The present study revealed that dihydrotanshinone I (DHTI) competitively inhibits CYP1A1/CYP1B1 and noncompetitively inhibits CYP1A2. DHTI exhibits a preference for inhibiting the genotoxicity associated with E2 4-hydroxylation pathway mediated by CYP1B1, potentially reducing the risk of 4-OHE2-induced genotoxicity.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Yu Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Jingyu Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Guangyun Ran
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Zihao Cheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Xin Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Yufen Liao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Xu Mao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Ying Peng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
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14
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Li KL, Liang YM, Chen Z, Zheng PJ, Zhang GQ, Yan B, Elshikh MS, Rizwana H, Chen B, Xu Q. Genome-wide identification of the alkaloid synthesis gene family CYP450, gives new insights into alkaloid resource utilization in medicinal Dendrobium. Int J Biol Macromol 2024; 259:129229. [PMID: 38211913 DOI: 10.1016/j.ijbiomac.2024.129229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
The medicinal Dendrobium species of Orchidaceae possess significant pharmaceutical value, and modern pharmacological research has shown that Dendrobium contains many important active ingredients. Alkaloids, the crucial components of medicinal Dendrobium, demonstrate beneficial healing properties in cardiovascular, cataract, gastrointestinal, and respiratory diseases. Members of the cytochrome P450 monooxygenase (CYP) gene family play essential roles in alkaloid synthesis, participating in alkaloid terpene skeleton construction and subsequent modifications. Although studies of the CYP family have been conducted in some species, genome-wide characterization and systematic analysis of the CYP family in medicinal Dendrobium remain underexplored. In this study, we identified CYP gene family members in the genomes of four medicinal Dendrobium species recorded in the Pharmacopoeia: D. nobile, D. chrysotoxum, D. catenatum, and D. huoshanense. Further, we analyzed the motif composition, gene replication events, and selection pressure of this family. Syntenic analysis revealed that members of the clan 710 were present on chromosome 18 in three medicinal Dendrobium species, except for D. nobile, indicating a loss of clan 710 occurring in D. nobile. We also conducted an initial screening of the CYP genes involved in alkaloid synthesis through transcriptome sequencing. Quantitative real-time reverse transcription PCR showed that the expression of DnoNew43 and DnoNew50, homologs of secologanin synthase involved in the alkaloid synthesis pathway, was significantly higher in the stems than in the leaves. This result coincided with the distribution of dendrobine content in Dendrobium stems and leaves, indicating that these two genes might be involved in the dendrobine synthesis pathway. Our results give insights into the CYP gene family evolution analysis in four medicinal Dendrobium species for the first time and identify two related genes that may be involved in alkaloid synthesis, providing a valuable resource for further investigations into alkaloid synthesis pathway in Dendrobium and other medicinal plants.
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Affiliation(s)
- Kang-Li Li
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China
| | - Yu-Min Liang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China
| | - Zhi Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China
| | - Pei-Ji Zheng
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binghua Yan
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mohamed Soliman Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Humaira Rizwana
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - BingJie Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China.
| | - Qing Xu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China.
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15
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Tarigholizadeh S, Sushkova S, Rajput VD, Ranjan A, Arora J, Dudnikova T, Barbashev A, Mandzhieva S, Minkina T, Wong MH. Transfer and Degradation of PAHs in the Soil-Plant System: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:46-64. [PMID: 38108272 DOI: 10.1021/acs.jafc.3c05589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, persistent organic pollutants that threaten ecosystems and human health. Consistent monitoring is essential to minimize the entry of PAHs into plants and reduce food chain contamination. PAHs infiltrate plants through multiple pathways, causing detrimental effects and triggering diverse plant responses, ultimately increasing either toxicity or tolerance. Primary plant detoxification processes include enzymatic transformation, conjugation, and accumulation of contaminants in cell walls/vacuoles. Plants also play a crucial role in stimulating microbial PAHs degradation by producing root exudates, enhancing bioavailability, supplying nutrients, and promoting soil microbial diversity and activity. Thus, synergistic plant-microbe interactions efficiently decrease PAHs uptake by plants and, thereby, their accumulation along the food chain. This review highlights PAHs uptake pathways and their overall fate as contaminants of emerging concern (CEC). Understanding plant uptake mechanisms, responses to contaminants, and interactions with rhizosphere microbiota is vital for addressing PAH pollution in soil and ensuring food safety and quality.
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Affiliation(s)
| | - Svetlana Sushkova
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Vishnu D Rajput
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Anuj Ranjan
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Jayati Arora
- Amity Institute of Environmental Science, Amity University, Noida 201301, India
| | - Tamara Dudnikova
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Andrey Barbashev
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | | | - Tatiana Minkina
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Ming Hung Wong
- Consortium on Health, Environment, Education, and Research (CHEER), The Education University of Hong Kong, Hong Kong, China; Southern Federal University, Rostov-on-Don, 344090, Russian Federation
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16
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Wang Z, Peng D, Fu C, Luo X, Guo S, Li L, Yin H. Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome. FRONTIERS IN PLANT SCIENCE 2023; 14:1248476. [PMID: 38179476 PMCID: PMC10765411 DOI: 10.3389/fpls.2023.1248476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.
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Affiliation(s)
- Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Changwu Fu
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xianxue Luo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Shijie Guo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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17
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Ma Y, Wang J, Liu Y, Wang X, Zhang B, Zhang W, Chen T, Liu G, Xue L, Cui X. Nocardioides: "Specialists" for Hard-to-Degrade Pollutants in the Environment. Molecules 2023; 28:7433. [PMID: 37959852 PMCID: PMC10649934 DOI: 10.3390/molecules28217433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Nocardioides, a genus belonging to Actinomycetes, can endure various low-nutrient conditions. It can degrade pollutants using multiple organic materials such as carbon and nitrogen sources. The characteristics and applications of Nocardioides are described in detail in this review, with emphasis on the degradation of several hard-to-degrade pollutants by using Nocardioides, including aromatic compounds, hydrocarbons, haloalkanes, nitrogen heterocycles, and polymeric polyesters. Nocardioides has unique advantages when it comes to hard-to-degrade pollutants. Compared to other strains, Nocardioides has a significantly higher degradation rate and requires less time to break down substances. This review can be a theoretical basis for developing Nocardioides as a microbial agent with significant commercial and application potential.
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Affiliation(s)
- Yecheng Ma
- College of Biotechnology and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xinyue Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Lingui Xue
- College of Biotechnology and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Xiaowen Cui
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
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18
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Kózka B, Sośnicka A, Nałęcz-Jawecki G, Drobniewska A, Turło J, Giebułtowicz J. Various species of Basidiomycota fungi reveal different abilities to degrade pharmaceuticals and also different pathways of degradation. CHEMOSPHERE 2023; 338:139481. [PMID: 37454990 DOI: 10.1016/j.chemosphere.2023.139481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The presence of pharmaceuticals (PhACs) in the aquatic environment is an emerging problem worldwide. PhACs reach surface water via the effluents of wastewater treatment plants (WWTPs). WWTPs, although able to remove organic pollutants, do not always remove PhACs. Currently, in the treatment of sewage with the activated sludge method, numerous microorganisms are used, mostly bacteria. Nevertheless, these microorganisms are not resistant to many drug contaminants, and some may also pose a risk to human health. White-rot fungi (WRF), which degrade a wide spectrum of environmental pollutants, may be used as an alternative to microorganisms. However, little data exists comparing the removal of various PhACs by different WRF. In this study, we aimed to determine the ability of three WRF Basidiomycota species, Armillaria mellea, Phanerochaete chrysosporium, and Pleurotus ostreatus, to remove PhACs from various therapeutic groups over the course of 1 h-4 days. Additionally, we identified the fungal metabolites of PhACs, proposed the degradation pathways, and assessed the toxicity of the post-culture media. All selected WRF removed PhACs, but the degree of removal depended on WRF species and PhACs type. Antidepressants and immunosuppressants were removed most efficiently by P. ostreatus, cardiovascular drugs and sulfamethoxazole by A. mellea, and erythromycin by P. chrysosporium. The vast differences observed highlight the need for more intensive testing of different WRF species to select the best species for removing pharmaceuticals of interest. The structure of metabolites generated during degradation strongly depended on WRF species, but the most frequent xenobiotic transformations were oxidation and dealkylation. The obtained results gave insight into the substrate specificity of selected WRF while also providing a broad extension of the knowledge of pharmaceutical degradation by A. mellea.
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Affiliation(s)
- B Kózka
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Poland
| | - A Sośnicka
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Technology and Pharmaceutical Biotechnology, Poland
| | - G Nałęcz-Jawecki
- Medical University of Warsaw, Faculty of Pharmacy, Department of Environmental Health Sciences, Poland
| | - A Drobniewska
- Medical University of Warsaw, Faculty of Pharmacy, Department of Environmental Health Sciences, Poland
| | - J Turło
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Technology and Pharmaceutical Biotechnology, Poland
| | - J Giebułtowicz
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Poland.
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19
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Zhang W, Li Q, Wang J, Wang Z, Zhan H, Yu X, Zheng Y, Xiao T, Zhou LW. Biodegradation of Benzo[a]pyrene by a White-Rot Fungus Phlebia acerina: Surfactant-Enhanced Degradation and Possible Genes Involved. J Fungi (Basel) 2023; 9:978. [PMID: 37888234 PMCID: PMC10607704 DOI: 10.3390/jof9100978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are persistent environmental pollutants that pose a threat to human health. Among these PAHs, benzo[a]pyrene (BaP), a five-ring compound, exhibits high resistance to biodegradation. White-rot fungus Phlebia acerina S-LWZ20190614-6 has demonstrated higher BaP degradation capabilities compared with Phanerochaete chrysosporium and P. sordida YK-624, achieving a degradation rate of 57.7% after 32 days of incubation under a ligninolytic condition. To further enhance the biodegradation rate, three nonionic surfactants were used, and the addition of 1 or 2 g·L-1 of polyethylene glycol monododecyl ether (Brij 30) resulted in nearly complete BaP biodegradation by P. acerina S-LWZ20190614-6. Interestingly, Brij 30 did not significantly affect the activity of manganese peroxidase and lignin peroxidase, but it did decrease laccase activity. Furthermore, the impact of cytochrome P450 on BaP degradation by P. acerina S-LWZ20190614-6 was found to be relatively mild. Transcriptomic analysis provided insights into the degradation mechanism of BaP, revealing the involvement of genes related to energy production and the synthesis of active enzymes crucial for BaP degradation. The addition of Brij 30 significantly upregulated various transferase and binding protein genes in P. acerina S-LWZ20190614-6. Hence, the bioremediation potential of BaP by the white-rot fungus P. acerina S-LWZ20190614-6 holds promise and warrants further exploration.
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Affiliation(s)
- Wenquan Zhang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Qiaoyu Li
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Jianqiao Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Ziyu Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Hongjie Zhan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Xiaolong Yu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu 610059, China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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20
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Khan MF, Hof C, Niemcová P, Murphy CD. Recent advances in fungal xenobiotic metabolism: enzymes and applications. World J Microbiol Biotechnol 2023; 39:296. [PMID: 37658215 PMCID: PMC10474215 DOI: 10.1007/s11274-023-03737-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
Fungi have been extensively studied for their capacity to biotransform a wide range of natural and xenobiotic compounds. This versatility is a reflection of the broad substrate specificity of fungal enzymes such as laccases, peroxidases and cytochromes P450, which are involved in these reactions. This review gives an account of recent advances in the understanding of fungal metabolism of drugs and pollutants such as dyes, agrochemicals and per- and poly-fluorinated alkyl substances (PFAS), and describes the key enzymes involved in xenobiotic biotransformation. The potential of fungi and their enzymes in the bioremediation of polluted environments and in the biocatalytic production of important compounds is also discussed.
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Affiliation(s)
- Mohd Faheem Khan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Carina Hof
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Patricie Niemcová
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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21
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Agustinus B, Gillam EMJ. Solar-powered P450 catalysis: Engineering electron transfer pathways from photosynthesis to P450s. J Inorg Biochem 2023; 245:112242. [PMID: 37187017 DOI: 10.1016/j.jinorgbio.2023.112242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
With the increasing focus on green chemistry, biocatalysis is becoming more widely used in the pharmaceutical and other chemical industries for sustainable production of high value and structurally complex chemicals. Cytochrome P450 monooxygenases (P450s) are attractive biocatalysts for industrial application due to their ability to transform a huge range of substrates in a stereo- and regiospecific manner. However, despite their appeal, the industrial application of P450s is limited by their dependence on costly reduced nicotinamide adenine dinucleotide phosphate (NADPH) and one or more auxiliary redox partner proteins. Coupling P450s to the photosynthetic machinery of a plant allows photosynthetically-generated electrons to be used to drive catalysis, overcoming this cofactor dependency. Thus, photosynthetic organisms could serve as photobioreactors with the capability to produce value-added chemicals using only light, water, CO2 and an appropriate chemical as substrate for the reaction/s of choice, yielding new opportunities for producing commodity and high-value chemicals in a carbon-negative and sustainable manner. This review will discuss recent progress in using photosynthesis for light-driven P450 biocatalysis and explore the potential for further development of such systems.
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Affiliation(s)
- Bernadius Agustinus
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia.
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22
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Laothanachareon T, Kongtong K, Saeng-Kla K, Kanokratana P, Leetanasaksakul K, Champreda V. Evaluating the efficacy of wood decay fungi and synthetic fungal consortia for simultaneous decolorization of multiple textile dyes. World J Microbiol Biotechnol 2023; 39:226. [PMID: 37316623 DOI: 10.1007/s11274-023-03672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/03/2023] [Indexed: 06/16/2023]
Abstract
Wastewater from the textile industry dyeing process containing high loads of synthetic dyes leads to pollution of water with these toxic and genotoxic dyes. Much effort has been put towards developing biological systems to resolve this issue. Mycoremediation is a well-known approach using fungi to remove, degrade, or remediate pollutants and can be applied to decolorize textile dyes in industrial effluent. Fungal strains from four genera of Polyporales, namely Coriolopsis sp. TBRC 2756, Fomitopsis pinicola TBRC-BCC 30881, Rigidoporus vinctus TBRC 6770, and Trametes pocas TBRC-BCC 18705, were studied for decolorization efficiency, and R. vinctus was found to exhibit the greatest activity in removing all seven tested reactive dyes and one acid dye with a decolorization efficiency of 80% or more within 7 days under limited oxygen. This fungus simultaneously degraded multiple dyes in synthetic wastewater as well as industrial effluent from the dyeing process. To enhance the decolorization rate, various fungal consortia were formulated for testing. However, these consortia only trivially improved efficiency compared with using R. vinctus TBRC 6770 alone. Evaluation of R. vinctus TBRC 6770 decolorization ability was further performed in a 15-L bioreactor to test its ability to eliminate multiple dyes from industrial effluent. The fungus took 45 days to adapt to growth in the bioreactor and subsequently reduced dye concentration to less than 10% of the initial concentration. The following six cycles required only 4-7 days to reduce dye concentrations to less than 25%, demonstrating that the system can run efficiently for multiple cycles without the need for extra medium or other carbon sources.
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Affiliation(s)
- Thanaporn Laothanachareon
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand.
| | - Kittima Kongtong
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Kanphorn Saeng-Kla
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Pattanop Kanokratana
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Kantinan Leetanasaksakul
- Functional Proteomics Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
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23
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Dai Y, Li J, Yang X, Wang S, Zhao X, Wang Y, Zhang D, Luo C, Zhang G. New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131271. [PMID: 36989785 DOI: 10.1016/j.jhazmat.2023.131271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Autochthonous fungal bioaugmentation (AFB) is considered a reliable bioremediation approach for polycyclic aromatic hydrocarbon (PAH) contamination, but little is known about its mechanisms in contaminated soils. Here, a microcosm experiment was performed to explore the AFB mechanisms associated with two highly efficient phenanthrene degrading agents of fungi (with laccase-producing Scedosporium aurantiacum GIG-3 and non-laccase-producing Aspergillus fumigatus LJD-29), using stable-isotope-probing (SIP) and high-throughput sequencing. The results showed that each fungus markedly improved phenanthrene removal, and microcosms with both fungi exhibited the best phenanthrene removal performance among all microcosms. Additionally, AFB markedly shifted the composition of the microbial community, particularly the phenanthrene-degrading bacterial taxa. Interestingly, based on SIP results, strains GIG-3 and LJD-29 did not assimilate phenanthrene directly during AFB, but instead played key roles in the preliminary decomposition of phenanthrene though secretion of different extracellular enzymes to oxidize the benzene ring (GIG-3 bioaugmentation with laccase, and LJD-29 bioaugmentation with manganese and lignin peroxidases). In addition, all functional degraders directly involved in phenanthrene assimilation were indigenous bacteria, while native fungi rarely participated in the direct phenanthrene mineralization. Our findings provide a new mechanism of AFB with multiple fungi, and support AFB as a promising strategy for the in situ bioremediation of PAH-contaminated soil.
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Affiliation(s)
- Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Xiumin Yang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Shuang Wang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xuan Zhao
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yujie Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
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24
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Merino N, Wang N, Gao Y, Wang M, Mahendra S. Roles of various enzymes in the biotransformation of 6:2 fluorotelomer alcohol (6:2 FTOH) by a white-rot fungus. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131007. [PMID: 36871371 DOI: 10.1016/j.jhazmat.2023.131007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Six-carbon-chained polyfluoroalkyl substances, such as 6:2 fluorotelomer alcohol (6:2 FTOH), are being used to replace longer chained compounds in the manufacture of various commercial products. This study examined the effects of growth substrates and nutrients on specific intracellular and extracellular enzymes mediating 6:2 FTOH aerobic biotransformation by the white-rot fungus, Phanerochaete chrysosporium. Cellulolytic conditions with limited glucose were a suitable composition, resulting in high 5:3 FTCA yield (37 mol%), which is a key intermediate in 6:2 FTOH degradation without forming significant amounts of terminal perfluorocarboxylic acids (PFCAs). Sulfate and ethylenediaminetetraacetic acid (EDTA) were also essential for 5:3 FTCA production, but, at lower levels, resulted in the buildup of 5:2 sFTOH (52 mol%) and 6:2 FTUCA (20 mol%), respectively. In non-ligninolytic nutrient-rich medium, 45 mol% 6:2 FTOH was transformed but produced only 12.7 mol% 5:3 FTCA. Enzyme activity studies imply that cellulolytic conditions induce the intracellular cytochrome P450 system. In contrast, extracellular peroxidase synthesis is independent of 6:2 FTOH exposure. Gene expression studies further verified that peroxidases were relevant in catalyzing the downstream transformations from 5:3 FTCA. Collectively, the identification of nutrients and enzymatic systems will help elucidate underlying mechanisms and biogeochemical conditions favorable for fungal transformation of PFCA precursors in the environment.
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Affiliation(s)
- Nancy Merino
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Ning Wang
- DuPont Haskell Global Centers for Health and Environmental Sciences, Newark, DE 19711, United States
| | - Yifan Gao
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Meng Wang
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States.
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25
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Ming Q, Huang X, He Y, Qin L, Tang Y, Liu Y, Huang Y, Zhang H, Li P. Genome Mining and Screening for Secondary Metabolite Production in the Endophytic Fungus Dactylonectria alcacerensis CT-6. Microorganisms 2023; 11:microorganisms11040968. [PMID: 37110391 PMCID: PMC10142127 DOI: 10.3390/microorganisms11040968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Endophytic fungi are a treasure trove of natural products with great chemical diversity that is largely unexploited. As an alternative to the traditional bioactivity-guided screening approach, the genome-mining-based approach provides a new methodology for obtaining novel natural products from endophytes. In our study, the whole genome of an endophyte, Dactylonectria alcacerensis CT-6, was obtained for the first time. Genomic analysis indicated that D. alcacerensis CT-6 has one 61.8 Mb genome with a G+C content of 49.86%. Gene annotation was extensively carried out using various BLAST databases. Genome collinearity analysis revealed that D. alcacerensis CT-6 has high homology with three other strains of the Dactylonectria genus. AntiSMASH analysis displayed 45 secondary metabolite biosynthetic gene clusters (BGCs) in D. alcacerensis CT-6, and most of them were unknown and yet to be unveiled. Furthermore, only six known substances had been isolated from the fermented products of D. alcacerensis CT-6, suggesting that a great number of cryptic BGCs in D. alcacerensis CT-6 are silent and/or expressed at low levels under conventional conditions. Therefore, our study provides an important basis for further chemical study of D. alcacerensis CT-6 using the gene-mining strategy to awaken these cryptic BGCs for the production of bioactive secondary metabolites.
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Affiliation(s)
- Qianliang Ming
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
- Drug and Instrument Supervision and Inspection Station, 32339 Troops of the Chinese People's Liberation Army, Lhasa 850015, China
| | - Xiuning Huang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yimo He
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Lingyue Qin
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yu Tang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yanxia Liu
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yuting Huang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Hongwei Zhang
- Drug and Instrument Supervision and Inspection Station, 32339 Troops of the Chinese People's Liberation Army, Lhasa 850015, China
| | - Peng Li
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
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26
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Chen S, Zhu M, Guo X, Yang B, Zhuo R. Coupling of Fenton reaction and white rot fungi for the degradation of organic pollutants. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114697. [PMID: 36889210 DOI: 10.1016/j.ecoenv.2023.114697] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Advanced oxidation processes (AOPs) are a class of highly efficient pollution remediation technologies that produce oxidising radicals under specific conditions to degrade organic pollutants. The Fenton reaction is a commonly applied AOP. To combine the advantages of AOPs and biodegradation in the remediation of organic pollutants, some studies have developed coupled systems between Fenton AOPs and white rot fungi (WRF) for environmental organic pollutant remediation and have achieved some success. Moreover, a promising system, termed as advanced bio-oxidation processes (ABOPs), mediated by the quinone redox cycling of WRF, has attracted increasing attention in the field. In this ABOP system, the radicals and H2O2 produced through the quinone redox cycling of WRF can strengthen Fenton reaction. Meanwhile, in this process, the reduction of Fe3+ to Fe2+ ensures the maintenance of Fenton reaction, leading to a promising application potential for the remediation of environmental organic pollutants. ABOPs combine the advantages of bioremediation and advanced oxidation remediation. Further understanding the coupling of Fenton reaction and WRF in the degradation of organic pollutants will be of great significance for the remediation of organic pollutants. Therefore, in this study, we reviewed recent remediation techniques for organic pollutants involving the coupled application of WRF and the Fenton reaction, focusing on the application of new ABOPs mediated by WRF, and discussed the reaction mechanism and conditions of ABOPs. Finally, we discussed the application prospects and future research directions of the joint application of WRF and advanced oxidation technologies for the remediation of environmental organic pollutants.
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Affiliation(s)
- Shuxian Chen
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China
| | - Mingdong Zhu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Hunan Rice Research Institute, Changsha 410125, PR China
| | - Xiayu Guo
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya, Sanya 572000, PR China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, PR China
| | - Bentao Yang
- Zhongye Changtian International Engineering Co., Ltd., Changsha 410205, PR China.
| | - Rui Zhuo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, PR China.
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27
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Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
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Shang C, Chen A, Cao R, Luo S, Shao J, Zhang J, Peng L, Huang H. Response of microbial community to the remediation of neonicotinoid insecticide imidacloprid contaminated wetland soil by Phanerochaete chrysosporium. CHEMOSPHERE 2023; 311:136975. [PMID: 36283437 DOI: 10.1016/j.chemosphere.2022.136975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/06/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Imidacloprid (IMI), a typic neonicotinoid insecticide, is widely used and persist in soils with long half-time causing serious threat to ecosystem and human health. It is urgent to develop suitable and effective methods to accelerate it degradation and alleviate its negative impacts in soil. In this study, the introduction of functional microbe white-rot fungus Phanerochaete chrysosporium to remediate IMI contaminated wetland soil was carried out. The remediation performance and the response of the soil microbial community were examined. The results showed that P. chrysosporium could improve the degradation of IMI in soil no matter the soil was sterilized or not. The bioaugmentation was especially observed in non-sterilized soil under the inoculation patterns of FE and SP with the maximum IMI degradation rate of 91% and 93% in 7 days, respectively. The invertase activity in soil was also enhanced with P. chrysosporium inoculation. Microbial community analysis revealed that P. chrysosporium inoculation could increase the diversity and richness of bacterial community, and stimulate some IMI degraders genera including Ochrobactrum, Leifsonia, Achromobacter, and Bacillus. Moreover, the xenobiotic degradation and metabolism pathway was generally enhanced with P. chrysosporium inoculation based on PICRUSt analysis. These obtained results demonstrated that the introduction of white-rot fungus is of great potentially enabling the remediation of neonicotinoids contaminated soil.
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Affiliation(s)
- Cui Shang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Anwei Chen
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Ruoyu Cao
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Si Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Jihai Shao
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Liang Peng
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Hongli Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
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Hu K, Li J, Zhao T, Zhou Q, Li Q, Hu X, Han G, Li S, Zou L, Liu S. Transcriptomic analysis reveals peripheral pathway in 3-phenoxybenzoic acid degradation by Aspergillus oryzae M-4. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116626. [PMID: 36327606 DOI: 10.1016/j.jenvman.2022.116626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
As a major intermediate metabolite of synthetic pyrethroids, the occurrence of 3-phenoxybenzoic acid hinders the decomposition of the parent pesticide and poses uncertain risks to environmental ecology and living organisms. Strain Aspergillus oryzae M-4 was previously reported to degrade 3-PBA and several substances were identified as downstream transformation products (TPs). But the mechanism underlying the cleavage of ether bond remains largely unclear. Here, we attempted to address such concern through identifying the peripheral TPs and analyzing transcriptomics, coupled with serial batch degradation experiments. Analysis results of chromatographic/mass spectrometry suggested that 3-PBA underwent twice hydroxylation, to yield mono- and dihydroxylated 3-PBA successively. In parallel, a mutual transformation between 3-PBA and 3-phenoxybenzyl alcohol (3-PBOH) also existed. The proposal of peripheral pathway represents an important advance towards fully understanding the whole 3-PBA metabolism in M-4. A specific altered metabolization was found for the first time, that is, resting cells of M-4 skipped the reduction step and initiate hydroxylation directly, by comparison with growing cells. Transcriptome analysis indicated that 3-PBA induced the up-regulation of genes related to energy investment, oxidative stress response, membrane transport and DNA repair. In-depth functional interpretation of differential expression genes suggested that the generation 3-PBOH and hydroxylated 3-PBA may be due to the participation of flavin-dependent monooxygenases (FMOs) and cytochrome P450 (CYP450), respectively. This study provides new insight to reveal the biodegradation mechanism of 3-PBA by A. oryzae M-4.
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Affiliation(s)
- Kaidi Hu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Jianlong Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Tianye Zhao
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Qiao Zhou
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Qin Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Xinjie Hu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Guoquan Han
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Shuhong Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China.
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Li L, Peng S, Wang Z, Zhang T, Li H, Xiao Y, Li J, Liu Y, Yin H. Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT. FRONTIERS IN PLANT SCIENCE 2022; 13:1025122. [PMID: 36407614 PMCID: PMC9667741 DOI: 10.3389/fpls.2022.1025122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | | | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- Hunan Urban and Rural Environmental Construction Co., Ltd, Changsha, China
| | - Hongguang Li
- Hunan Tobacco Science Institute, Changsha, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Jingjun Li
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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