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Egbewale SO, Kumar A, Mokoena MP, Olaniran AO. Purification, characterization and three-dimensional structure prediction of multicopper oxidase Laccases from Trichoderma lixii FLU1 and Talaromyces pinophilus FLU12. Sci Rep 2024; 14:13371. [PMID: 38862560 PMCID: PMC11167041 DOI: 10.1038/s41598-024-63959-z] [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: 03/04/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Broad-spectrum biocatalysts enzymes, Laccases, have been implicated in the complete degradation of harmful pollutants into less-toxic compounds. In this study, two extracellularly produced Laccases were purified to homogeneity from two different Ascomycetes spp. Trichoderma lixii FLU1 (TlFLU1) and Talaromyces pinophilus FLU12 (TpFLU12). The purified enzymes are monomeric units, with a molecular mass of 44 kDa and 68.7 kDa for TlFLU1 and TpFLU12, respectively, on SDS-PAGE and zymogram. It reveals distinct properties beyond classic protein absorption at 270-280 nm, with TlFLU1's peak at 270 nm aligning with this typical range of type II Cu site (white Laccase), while TpFLU12's unique 600 nm peak signifies a type I Cu2+ site (blue Laccase), highlighting the diverse spectral fingerprints within the Laccase family. The Km and kcat values revealed that ABTS is the most suitable substrate as compared to 2,6-dimethoxyphenol, caffeic acid and guaiacol for both Laccases. The bioinformatics analysis revealed critical His, Ile, and Arg residues for copper binding at active sites, deviating from the traditional two His and a Cys motif in some Laccases. The predicted biological functions of the Laccases include oxidation-reduction, lignin metabolism, cellular metal ion homeostasis, phenylpropanoid catabolism, aromatic compound metabolism, cellulose metabolism, and biological adhesion. Additionally, investigation of degradation of polycyclic aromatic hydrocarbons (PAHs) by purified Laccases show significant reductions in residual concentrations of fluoranthene and anthracene after a 96-h incubation period. TlFLU1 Laccase achieved 39.0% and 44.9% transformation of fluoranthene and anthracene, respectively, while TpFLU12 Laccase achieved 47.2% and 50.0% transformation, respectively. The enzyme structure-function relationship study provided insights into the catalytic mechanism of these Laccases for possible biotechnological and industrial applications.
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Affiliation(s)
- Samson O Egbewale
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, 4001, South Africa
| | - Ajit Kumar
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, 4001, South Africa
| | - Mduduzi P Mokoena
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, 4001, South Africa
- Department of Pathology, School of Medicine, University of Limpopo, Private Bag X1106, Sovenga, 0727, South Africa
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, 4001, South Africa.
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Elmetwalli A, Allam NG, Hassan MG, Albalawi AN, Shalaby A, El-Said KS, Salama AF. Evaluation of Bacillus aryabhattai B8W22 peroxidase for phenol removal in waste water effluents. BMC Microbiol 2023; 23:119. [PMID: 37120512 PMCID: PMC10148497 DOI: 10.1186/s12866-023-02850-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023] Open
Abstract
Environmental contamination by phenol has been reported in both aquatic and atmospheric environments. This study aimed to separate and purify the peroxidase enzyme from bacteria that degrade phenol from wastewater sources. An enrichment culture of MSM was used to screen 25 bacterial isolates from different water samples for peroxidase production, six of the isolates exhibited high levels of peroxidase enzyme activity. Qualitative analysis of peroxidase revealed that isolate No. 4 had the highest halo zones (Poly-R478: 14.79 ± 0.78 mm, Azure B: 8.81 ± 0.61 mm). The promising isolate was identified as Bacillus aryabhattai B8W22 by 16S rRNA gene sequencing with accession number OP458197. As carbon and nitrogen sources, mannitol and sodium nitrate were utilized to achieve maximum peroxidase production. A 30-h incubation period was used with pH 6.0, 30 °C, mannitol, and sodium nitrate, respectively, for maximal production of peroxidase. Purified peroxidase enzyme showed 0.012 U/mg specific activity, and SDS-PAGE analysis indicated a molecular weight of 66 kDa. The purified enzyme exhibits maximum activity and thermal stability at pH values of 4.0 and 8.0, respectively, with maximum activity at 30 °C and complete thermal stability at 40 °C. In the purified enzyme, the Km value was 6.942 mg/ml and the Vmax value was 4.132 mol/ml/hr, respectively. The results demonstrated that Bacillus aryabhattai B8W22 has promising potential for degrading phenols from various phenol-polluted wastewater sources.
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Affiliation(s)
- Alaa Elmetwalli
- Department of Clinical Trial Research Unit and Drug Discovery, Egyptian Liver Research Institute and Hospital (ELRIAH), Mansoura, Egypt.
| | - Nanis G Allam
- Microbiology Division, Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mervat G Hassan
- Department of Botany and Microbiology, Faculty of Science, Benha University, Benha, 33516, Egypt
| | - Aisha Nawaf Albalawi
- Department of Biology , University of Haql College, University of Tabuk, Tabuk, 71491, Saudi Arabia
| | - Azza Shalaby
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Karim Samy El-Said
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Afrah Fatthi Salama
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
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Khedr M, Khalil KMA, Kabary HA, Hamed AA, Badawy MSEM, Abu-Elghait M. Molecular docking and nucleotide sequencing of successive expressed recombinant fungal peroxidase gene in E.coli. J Genet Eng Biotechnol 2022; 20:94. [PMID: 35776246 PMCID: PMC9249955 DOI: 10.1186/s43141-022-00377-6] [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: 03/12/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022]
Abstract
Background Fungal peroxidases are oxidoreductases that utilize hydrogen peroxide to catalyze lignin biodegradation. Results PER-K (peroxidase synthesis codon gene) was transformed from Aspergillus niger strain AN512 deposited in the National Center for Biotechnology Information with the accession number OK323140 to Escherichia coli strain (BL21-T7 with YEp356R recombinant plasmid) via calcium chloride heat-shock method. The impact of four parameters (CaCl2 concentrations, centrifugation time, shaking speed, growth intensity) on the efficacy of the transformation process was evaluated. Furthermore, peroxidase production after optimization was assessed both qualitatively and quantitatively, as well as SDS-PAGE analysis. The optimum conditions for a successful transformation process were as follows: CaCl2 concentrations (50 mM), centrifugation time (20 min), shaking speed (200 rpm), and growth optical density (0.45). PCR and gel electrophoresis detect DNA bands with lengths 175, 179, and 211 bps corresponding to UA3, AmpR, and PER-K genes respectively besides partially sequencing the PER-K gene. Pyrogallol/hydrogen peroxide assay confirmed peroxidase production, and the activity of the enzyme was determined to be 3924 U/L. SDS-PAGE analysis also confirms peroxidase production illustrated by the appearance of a single peroxidase protein band after staining with Coomassie blue R-250. Conclusion A successful peroxidase-gene (PER-K) transformation from fungi to bacteria was performed correctly. The enzyme activity was screened, and partial sequencing of PER-K gene was analyzed successively. The protein 3D structure was generated via in silico homology modeling, and determination of binding sites and biological annotations of the constructed protein were carried out via COACH and COFACTOR based on the I-TASSER structure prediction. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00377-6.
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Affiliation(s)
- Mohamed Khedr
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt
| | - Kamal M A Khalil
- Genetic Engineering and Biotechnology Division, Genetics and Cytology Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Hoda A Kabary
- Agricultural Microbiology Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Ahmed A Hamed
- Microbial Chemistry Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Mona Shaban E M Badawy
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Mohammed Abu-Elghait
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt.
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Maibeche R, Boucherba N, Bendjeddou K, Prins A, Bouiche C, Hamma S, Benhoula M, Azzouz Z, Bettache A, Benallaoua S, Le Roes-Hill M. Peroxidase-producing actinobacteria from Algerian environments and insights from the genome sequence of peroxidase-producing Streptomyces sp. S19. Int Microbiol 2022; 25:379-396. [DOI: 10.1007/s10123-022-00236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/08/2021] [Accepted: 01/17/2022] [Indexed: 11/28/2022]
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Rath S, Paul M, Behera HK, Thatoi H. Response surface methodology mediated optimization of Lignin peroxidase from Bacillus mycoides isolated from Simlipal Biosphere Reserve, Odisha, India. J Genet Eng Biotechnol 2022; 20:2. [PMID: 34978643 PMCID: PMC8724326 DOI: 10.1186/s43141-021-00284-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Lignin is a complex polymer of phenyl propanoid units found in the vascular tissues of the plants as one of lignocellulose materials. Many bacteria secrete enzymes to lyse lignin, which can be essential to ease the production of bioethanol. Current research focused on the study of ligninolytic bacteria capable of producing lignin peroxidase (LiP) which can help in lignin biodegradation and bioethanol production. Ligninolytic bacterial strains were isolated and screened from the soil samples of Simlipal Biosphere Reserve (SBR), Odisha (India), for the determination of their LiP activity. Enzymatic assay and optimization for the LiP activity were performed with the most potent bacterial strain. The strain was identified by morphological, biochemical, and molecular methods. RESULTS In this study, a total of 16 bacteria (Simlipal ligninolytic bacteria [SLB] 1-16) were isolated from forest soils of SBR using minimal salt medium containing lignin. Out of the 16 isolates, 9 isolates showed decolourization of methylene blue dye on LB agar plates. The bacterial isolates such as SLB8, SLB9, and SLB10 were able to decolourize lignin with 15.51%, 16.80%, and 33.02%, respectively. Further enzyme assay was performed using H2O2 as substrate and methylene blue as an indicator for these three bacterial strains in lignin containing minimal salt medium where the isolate SLB10 showed the highest LiP activity (31.711 U/mg). The most potent strain, SLB10, was optimized for enhanced LiP enzyme activity using response surface methodology. In the optimized condition of pH 10.5, temperature 30 °C, H2O2 concentration 0.115 mM, and time 42 h, SLB10 showed a maximum LiP activity of 55.947 U/mg with an increase of 1.76 times from un-optimized condition. Further chemical optimization was performed, and maximum LiP activity as well as significant dye-decolourization efficiency of SLB10 has been found in bacterial growth medium supplemented individually with cellulose, yeast extract, and MnSO4. Most notably, yeast extract and MnSO4-supplemented bacterial culture medium were shown to have even higher percentage of dye decolourization compared to normal basal medium. The bacterial strain SLB10 was identified as Bacillus mycoides according to morphological, biochemical, and molecular (16S rRNA sequencing) characterization and phylogenetic tree analysis. CONCLUSION Result from the present study revealed the potential of Bacillus mycoides bacterium isolated from the forest soil of SBR in producing LiP enzyme that can be evaluated further for application in lignin biodegradation and bioethanol production. Scaling up of LiP production from this potent bacterial strain could be useful in different industrial applications.
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Affiliation(s)
- Subhashree Rath
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada, Odisha, 757003, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada, Odisha, 757003, India
| | - Hemanta Kumar Behera
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada, Odisha, 757003, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada, Odisha, 757003, India.
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Abstract
Global demand for renewable and sustainable energy is increasing, and one of the most common biofuels is ethanol. Most ethanol is produced by Saccharomyces cerevisiae (yeast) fermentation of either crops rich in sucrose (e.g., sugar cane and sugar beet) or starch-rich crops (e.g., corn and starchy grains). Ethanol produced from these sources is termed a first-generation biofuel. Yeast fermentation can yield a range of additional valuable co-products that accumulate during primary fermentation (e.g., protein concentrates, water soluble metabolites, fusel alcohols, and industrial enzymes). Distillers’ solubles is a liquid co-product that can be used in animal feed or as a resource for recovery of valuable materials. In some processes it is preferred that this fraction is modified by a second fermentation with another fermentation organism (e.g., lactic acid bacteria). Such two stage fermentations can produce valuable compounds, such as 1,3-propanediol, organic acids, and bacteriocins. The use of lactic acid bacteria can also lead to the aggregation of stillage proteins and enable protein aggregation into concentrates. Once concentrated, the protein has utility as a high-protein feed ingredient. After separation of protein concentrates the remaining solution is a potential source of several known small molecules. The purpose of this review is to provide policy makers, bioethanol producers, and researchers insight into additional added-value products that can be recovered from ethanol beers. Novel products may be isolated during or after distillation. The ability to isolate and purify these compounds can provide substantial additional revenue for biofuel manufacturers through the development of marketable co-products.
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Falade AO, Mabinya LV, Okoh AI, Nwodo UU. Agroresidues enhanced peroxidase activity expression by Bacillus sp. MABINYA-1 under submerged fermentation. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00345-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractAgroresidues have continued to gain preference over conventional carbon sources for microbial enzyme production due to the low price and abundance in the environment. Therefore, this study aimed at improving peroxidase yield by Bacillus sp. MABINYA-1 (BMAB-1) using agroresidues under submerged fermentation. The culture parameters that support maximum peroxidase yield by BMAB-1 was initially determined and the results showed that peroxidase activity expression was optimum at pH 5, 30 °C and 150 rpm while veratryl alcohol and ammonium sulphate served as the best peroxidase-inducer and inorganic nitrogen source, respectively. BMAB-1 exhibited maximum peroxidase expression (17.50 ± 0.10 U/mg) at 72 h using kraft lignin liquid medium (KLLM) under the optimized culture conditions. Upon utilization of selected agroresidues (sawdust, wheat straw and maize stover) as sole carbon sources by BMAB-1 in the fermentation process, peroxidase activity was significantly enhanced when compared with glucose (14.91 ± 0.31 U/mg) and kraft lignin (17.50 ± 0.10 U/mg). Sawdust produced the highest peroxidase yield (47.14 ± 0.41 U/mg), followed by maize stover (37.09 ± 0.00 U/mg) while wheat straw yielded the lowest peroxidase specific activity (21.65 ± 0.35 U/mg). This indicates that utilization of sawdust by BMAB-1 resulted in 3.2- and 2.7-fold increase in peroxidase activity expression as compared to glucose and kraft lignin, respectively. The aptitude of BMAB-1 to utilize agroresidues would reduce the cost of peroxidase production by the bacteria since the substrates are cheaper than the conventional carbon sources and are, as well, more readily available.
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Falade AO, Mabinya LV, Okoh AI, Nwodo UU. Studies on peroxidase production and detection of Sporotrichum thermophile-like catalase-peroxidase gene in a B acillus species isolated from Hogsback forest reserve, South Africa. Heliyon 2020; 5:e03012. [PMID: 31890960 PMCID: PMC6926187 DOI: 10.1016/j.heliyon.2019.e03012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/22/2019] [Accepted: 12/06/2019] [Indexed: 11/26/2022] Open
Abstract
This study sought to determine the process conditions for optimum peroxidase production by a Bacillus species (Bacillus sp. FALADE-1-KX640922) isolated from Hogsback forest reserve in South Africa and characterize the peroxidase gene in the bacteria. We optimized peroxidase production by manipulating the environmental and nutritional parameters under submerged fermentation. Subsequently, the gene encoding heme-peroxidase was determined through nested polymerase chain reaction and Sanger DNA sequencing. The studied bacteria had maximum peroxidase production at pH 8, 30 °C and 150 rpm. The addition of guaiacol to lignin fermentation medium enhanced peroxidase production by over 100 % in the studied bacteria. However, the other lignin monomers (veratryl alcohol, vanillin, vanillic acid and ferulic acid) repressed the enzyme activity. Modification of the fermentation medium with ammonium sulphate gave the maximum peroxidase yield (8.87 U mL−1). Under the predetermined culture conditions, Bacillus sp. FALADE-1 expressed maximum specific peroxidase activity at 48 h (8.32 U mg−1). Interestingly, a search of the sequenced gene in PeroxiBase showed 100% similarity to Sporotrichum thermophile catalase-peroxidase gene (katG), as well, the deduced protein sequence clustered with bacterial catalase-peroxidases and had a molecular weight of about 11.45 kDa with 7.01 as the estimated isoelectric point. Subsequently, the nucleotide sequence was deposited in the National Center for Biotechnology Information (NCBI) repository with the accession number MF407314. In conclusion, Bacillus sp. FALADE-1 is a promising candidate for improved peroxidase production.
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Affiliation(s)
- Ayodeji O. Falade
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa
- Department of Biochemistry, University of Medical Sciences, Ondo, 351101, Ondo State, Nigeria
- Corresponding author.
| | - Leonard V. Mabinya
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa
| | - Anthony I. Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa
| | - Uchechukwu U. Nwodo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa
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