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Rathour RK, Kiran, Thakur N, Bhatt AK, Bhatia RK. Bio-inspired multifunctional and reusable LiP@MFO-GO and LiP@MFO-Chit hybrid enzyme complexes for efficient degradation of melanin. Bioorg Chem 2024; 151:107629. [PMID: 39003942 DOI: 10.1016/j.bioorg.2024.107629] [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: 05/21/2024] [Revised: 06/29/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
Melanin is a complex brown pigment, primarily responsible for the skin pigmentation. Therefore, cosmetic industries have always been in search of potent oxidative enzymes useful for melanin degradation, and to promise a fair complexion after using their products. In the present study, lignin peroxidase from Pseudomonas fluorescence LiP-RL5 isolate has been immobilized on super-paramagnetic nanoparticles to enhance its stability and reusability. The chitosan coated enzyme-nanomaterial complex (LiP@MFO-Chit) showed higher melanin decolorization (47.30 ± 2.3 %) compared to the graphene oxide coated nanoparticles (LiP@MFO-GO) (41.60 ± 1.6 %). Synthesized enzyme nanoparticle complexes showed microbicidal effect on skin infection causing pathogen, Pantoea agglomerans with an inhibitory zone of 6.0 ± 0.9 mm and 250 µg/100 µl minimum inhibitory concentration, and a 7.0 ± 1.5 mm zone and 170 µg/100 µl MIC for LiP@MFO-GO and LiP@MFO-Chit, respectively. Antioxidant potential of LiP@MFO-Chit and LiP@MFO-GO nano-conjugates showed a substantial DPPH scavenging activity of 75.7 % and 88.3 %, respectively. Therefore, LiP-nanoparticle hybrid complexes analyzed in this study are not only effective as skin whitening agents but they are potential molecules against various microbial skin infections as well as useful for different other biomedical applications like biorefinery, drug delivery, and dermatology, etc.
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Affiliation(s)
- Ranju Kumari Rathour
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla 05, India; Department of Biotechnology, Chandigarh group of colleges, Landran, Mohali, India
| | - Kiran
- Department of Physics, Himachal Pradesh University, Summer Hill, Shimla 05, India
| | - Nagesh Thakur
- Department of Physics, Himachal Pradesh University, Summer Hill, Shimla 05, India
| | - Arvind Kumar Bhatt
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla 05, India
| | - Ravi Kant Bhatia
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla 05, India.
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2
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Brychcy M, Nguyen B, Tierney GA, Casula P, Kokodynski A, Godoy VG. The metabolite vanillic acid regulates Acinetobacter baumannii surface attachment. Mol Microbiol 2024; 121:833-849. [PMID: 38308563 DOI: 10.1111/mmi.15234] [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: 10/20/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/05/2024]
Abstract
The nosocomial bacterium Acinetobacter baumannii is protected from antibiotic treatment by acquiring antibiotic resistances and by forming biofilms. Cell attachment, one of the first steps in biofilm formation, is normally induced by environmental metabolites. We hypothesized that vanillic acid (VA), the oxidized form of vanillin and a widely available metabolite, may play a role in A. baumannii cell attachment. We first discovered that A. baumannii actively breaks down VA through the evolutionarily conserved vanABKP genes. These genes are under the control of the repressor VanR, which we show binds directly to VanR binding sites within the vanABKP genes bidirectional promoter. VA in turn counteracts VanR inhibition. We identified a VanR binding site and searched for it throughout the genome, especially in pili encoding promoter genes. We found a VanR binding site in the pilus encoding csu operon promoter and showed that VanR binds specifically to it. As expected, a strain lacking VanR overproduces Csu pili and makes robust biofilms. Our study uncovers the role that VA plays in facilitating the attachment of A. baumannii cells to surfaces, a crucial step in biofilm formation. These findings provide valuable insights into a previously obscure catabolic pathway with significant clinical implications.
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Affiliation(s)
- Merlin Brychcy
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Brian Nguyen
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | | | - Pranav Casula
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Alexis Kokodynski
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Veronica G Godoy
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
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3
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Riyadi FA, Azman NF, Nadia Md Akhir F, Othman N, Hara H. Identification and characterization of lignin depolymerization enzymes in Bacillus subtilis strain S11Y isolated from a tropical environment in Malaysia. J GEN APPL MICROBIOL 2024; 69:278-286. [PMID: 37612074 DOI: 10.2323/jgam.2023.08.003] [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] [Indexed: 08/25/2023]
Abstract
Biological pretreatment using microbial enzymes appears to be the most promising pre-treatment technology for the breakdown of recalcitrant lignin structure. This research focuses on the identification and characterization of lignin-depolymerizing enzymes in Bacillus subtilis strain S11Y, previously isolated from palm oil wastes in Malaysia. The draft genome sequences of this highly lignin-depolymerizing strain revealed that the genome lacked any of the well-known dye-decolorizing peroxidase or catalase-peroxidase that are commonly reported to be involved in lignin depolymerization by bacteria, indicating that strain S11Y has distinct sets of potential lignin depolymerization genes. The oxidative stress-related enzymes Cu/Zn type-superoxide dismutase (Sod2) and a heme-containing monofunctional catalase (Kat2) were identified in the genome sequences that are of interest. Their lignin-depolymerizing ability were evaluated by treating Alkali lignin (AL) with each enzyme and their degradation ability were evaluated using gel-permeation chromatography (GPC), ultrahigh-pressure liquid chromatography-mass spectrometry (UHPLC/MS), and gas chromatography-mass spectrometry (GC/MS), which successfully proved lignin depolymerizing ability. Successful evaluation of lignin depolymerizing enzymes can be applicable for lignin pretreatment process in green energy production and generation of valuable chemicals in bio-refinery.
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Affiliation(s)
- Fatimah Azizah Riyadi
- Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Nadia Farhana Azman
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Fazrena Nadia Md Akhir
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Nor'azizi Othman
- Department of Mechanical Precision Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Hirofumi Hara
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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4
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Pundee K, Akeprathumchai S, Tripetchkul S, Salaipeth L. Unveiling the microbial dynamics in vermicomposting with coir pith as earthworm substrate. Heliyon 2023; 9:e22945. [PMID: 38144354 PMCID: PMC10746422 DOI: 10.1016/j.heliyon.2023.e22945] [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: 07/22/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
This study explored the impact of incorporating coir pith, a byproduct of the coconut industry, into the vermicomposting substrate of Eudrilus eugeniae earthworms. The groups were compared based on their diets: cow manure only or cow manure mixed with varying amounts of coir pith. The aim was to assess the effects of coir pith on earthworm growth, mortality and the microbial community involved in vermicomposting. Earthworms fed with higher proportions of coir pith (70 % w/w) experienced reduced growth (0.81 g/worm) and increased mortality (24.67 %) after 5 weeks of vermicomposting. These effects were attributed to the high level of total phenolic content in the system. Coir pith required specific bacteria for digestion and detoxification, and excessive intake disrupted the earthworms' digestion, thus hindering nutrient absorption. The study also examined the microbial composition of the vermicast samples and identified variations based on the diet. Bacterial taxa involved in lignocellulose degradation, such as Bacteriodota, Azospirillum, Chitinophagaceae, Marinomonas and Pantoea, exhibited decreased abundances in treatments with coir pith. Conversely, the abundances of potentially harmful bacteria, such as Aeromonas, increased with higher coir pith inclusion levels. This pioneering investigation sheds light on the feasibility of coir pith use in vermicomposting and emphasises the importance of optimising earthworm diets to enhance microbial ecological functions and improve vermicompost quality.
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Affiliation(s)
- Kanokwan Pundee
- College of Multidisciplinary Sciences, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Saengchai Akeprathumchai
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Sudarut Tripetchkul
- Natural Resource Management and Sustainability Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Lakha Salaipeth
- Natural Resource Management and Sustainability Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
- LigniTech-Lignin Technology Research Group, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
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5
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Cagide C, Marizcurrena JJ, Vallés D, Alvarez B, Castro-Sowinski S. A bacterial cold-active dye-decolorizing peroxidase from an Antarctic Pseudomonas strain. Appl Microbiol Biotechnol 2023; 107:1707-1724. [PMID: 36773063 DOI: 10.1007/s00253-023-12405-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 02/12/2023]
Abstract
DyP (dye-decolorizing peroxidase) enzymes are hemeproteins that catalyze the H2O2-dependent oxidation of various molecules and also carry out lignin degradation, albeit with low activity. We identified a dyp gene in the genome of an Antarctic cold-tolerant microbe (Pseudomonas sp. AU10) that codes for a class B DyP. The recombinant protein (rDyP-AU10) was produced using Escherichia coli as a host and purified. We found that rDyP-AU10 is mainly produced as a dimer and has characteristics that resemble psychrophilic enzymes, such as high activity at low temperatures (20 °C) when using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and H2O2 as substrates, thermo-instability, low content of arginine, and a catalytic pocket surface larger than the DyPs from some mesophilic and thermophilic microbes. We also report the steady-state kinetic parameters of rDyP-AU10 for ABTS, hydroquinone, and ascorbate. Stopped-flow kinetics revealed that Compound I is formed with a rate constant of (2.07 ± 0.09) × 106 M-1 s-1 at pH 5 and that this is the predominant species during turnover. The enzyme decolors dyes and modifies kraft lignin, suggesting that this enzyme may have potential use in bioremediation and in the cellulose and biofuel industries. KEY POINTS: • An Antarctic Pseudomonas strain produces a dye-decolorizing peroxidase. • The recombinant enzyme (rDyP-AU10) was produced in E. coli and purified. • rDyP-AU10 showed high activity at low temperatures. • rDyP-AU10 is potentially useful for biotechnological applications.
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Affiliation(s)
- Célica Cagide
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Juan José Marizcurrena
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Diego Vallés
- Laboratorio de Biocatalizadores y sus Aplicaciones, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, and Centro de Investigaciones Biomédicas, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
- Laboratorio de Biocatalizadores y sus Aplicaciones, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
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Pan J, Han Y, Wang C, Du J, Wang Y, Chen Y, Huang X, Ma K, Zhang Z, Li N. Analysis of microbial community and biodeterioration of maritime cultural relics (ironware, porcelain, axes, hull wood) from the Nanhai No. 1 shipwreck. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-022-01705-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Abstract
Purpose
Maritime cultural relics from the Nanhai No. 1 shipwreck were immersed in a buffer to maintain stability. To better monitor the changes in the composition of microorganisms in the buffer and, thus, prevent the damage to artifacts caused by harmful microorganisms.
Methods
In September and November 2019, we conducted high-throughput sequencing of water samples from four types of maritime cultural relics (ironware, porcelain, axe, and hull wood) to reveal the composition and changes in microbial communities. In addition, we isolated culturable microorganisms and conducted biocide sensitivity tests and lignin and cellulose degradation tests.
Results
Visible microbial colonization was observed in the water samples collected from the buffer solutions of ironware, porcelain, axe, and hull wood of the Nanhai No. 1 shipwreck; additionally, apparent differences in the composition of microorganisms in the water samples collected from different cultural relics and different collection times of the same cultural relics were noted. Few species of bacteria and fungi from the microbial community observed in the maritime cultural relics were cultured, and it was noted that various biocides had certain inhibitory effects on them. Some dominant strains had lignin and cellulose degradation abilities and could only grow under specific environmental conditions.
Conclusion
We found apparent differences in the composition of microorganisms obtained from different cultural relics and different collection times of the same cultural relics. This study can provide data support for better protection of maritime cultural relics obtained from the Nanhai No. 1 shipwreck and provide a theoretical basis for the biological protection of other maritime cultural relics.
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7
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Unrean P, Champreda V. Optimized pulse-feeding fed-batch fermentation for enhanced lignin to polyhydroxyalkanoate transformation. Biotechnol Prog 2023; 39:e3302. [PMID: 36153640 DOI: 10.1002/btpr.3302] [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: 06/23/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/08/2022]
Abstract
With an anticipated growth of Bio-Circular-Green economy, the amount of lignin generated as by-product from biorefineries is increasing. Hence, lignin valorising strategies become a very interesting option to improve economic viability of the biorefineries. This study revealed the development of bioprocesses for upgrading lignin into bioplastic. Specifically, a novel strain of Pseudomonas fulva has been applied for microbial bioconversion of organosolv lignin to fermentative polyhydroxyalkanoate (PHA) production. Fed-batch fermentation of lignin-to-PHA with pulse-feeding approach was optimized using Design of Experiment. Effects of C:N ratio and feeding profiles on PHA accumulation in P. fulva were investigated to determine optimal operation. Under optimized fed-batch, the PHA concentration of 195.2 ± 6.6 mg/L could be reached and the PHA content was more than 2 folds enhancement compared to batch process. Type of PHA produced was also characterized for chemical composition via GC-MS analysis. The established lignin to PHA conversion could provide platform for developing integrated lignin bioprocessing to promote cost-effective biorefineries.
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Affiliation(s)
- Pornkamol Unrean
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
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8
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Adeniyi A, Bello I, Mukaila T, Hammed A. A Review of Microbial Molecular Profiling during Biomass Valorization. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Ma L, Wang X, Zhou J, Lü X. Degradation of switchgrass by Bacillus subtilis 1AJ3 and expression of a beta-glycoside hydrolase. Front Microbiol 2022; 13:922371. [PMID: 35966659 PMCID: PMC9374367 DOI: 10.3389/fmicb.2022.922371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing demand for carbon neutrality has led to the development of new techniques and modes of low carbon production. The utilization of microbiology to convert low-cost renewable resources into more valuable chemicals is particularly important. Here, we investigated the ability of a cellulolytic bacterium, Bacillus subtilis 1AJ3, in switchgrass lignocellulose degradation. After 5 days of culture with the strain under 37°C, cellulose, xylan, and acid-insoluble lignin degradation rates were 16.13, 14.24, and 13.91%, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis and field emission scanning electron microscopy (FE-SEM) indicated that the lignin and surface of switchgrass were degraded after incubation with the bacterial strain. Strain 1AJ3 can grow well below 60°C, which satisfies the optimum temperature (50°C) condition of most cellulases; subsequent results emphasize that acid-heat incubation conditions increase the reducing sugar content in a wide range of cellulosic biomass degraded by B. subtilis 1AJ3. To obtain more reducing sugars, we focused on β-glycoside hydrolase, which plays an important role in last steps of cellulose degradation to oligosaccharides. A β-glycoside hydrolase (Bgl-16A) was characterized by cloning and expression in Escherichia coli BL21 and further determined to belong to glycoside hydrolase (GH) 16 family. The Bgl-16A had an enzymatic activity of 365.29 ± 10.43 U/mg, and the enzyme's mode of action was explained by molecular docking. Moreover, the critical influence on temperature (50°C) of Bgl-16A also explained the high-efficiency degradation of biomass by strain under acid-heat conditions. In terms of potential applications, both the strain and the recombinant enzyme showed that coffee grounds would be a suitable and valuable substrate. This study provides a new understanding of cellulose degradation by B. subtilis 1AJ3 that both the enzyme action mode and optimum temperature limitation by cellulases could impact the degradation. It also gave new sight to unique advantage utilization in the industrial production of green manufacturing.
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Affiliation(s)
- Lingling Ma
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Xin Wang
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xin Lü
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Xianyang, China
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Recent Advances in Synthesis and Degradation of Lignin and Lignin Nanoparticles and Their Emerging Applications in Nanotechnology. MATERIALS 2022; 15:ma15030953. [PMID: 35160893 PMCID: PMC8838035 DOI: 10.3390/ma15030953] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 01/16/2023]
Abstract
Lignin is an important commercially produced polymeric material. It is used extensively in both industrial and agricultural activities. Recently, it has drawn much attention from the scientific community. It is abundantly present in nature and has significant application in the production of biodegradable materials. Its wide usage includes drug delivery, polymers and several forms of emerging lignin nanoparticles. The synthesis of lignin nanoparticles is carried out in a controlled manner. The traditional manufacturing techniques are costly and often toxic and hazardous to the environment. This review article highlights simple, safe, climate-friendly and ecological approaches to the synthesis of lignin nanoparticles. The changeable, complex structure and recalcitrant nature of lignin makes it challenging to degrade. Researchers have discovered a small number of microorganisms that have developed enzymatic and non-enzymatic metabolic pathways to use lignin as a carbon source. These microbes show promising potential for the biodegradation of lignin. The degradation pathways of these microbes are also described, which makes the study of biological synthesis much easier. However, surface modification of lignin nanoparticles is something that is yet to be explored. This review elucidates the recent advances in the biodegradation of lignin in the ecological system. It includes the current approaches, methods for modification, new applications and research for the synthesis of lignin and lignin nanoparticles. Additionally, the intricacy of lignin’s structure, along with its chemical nature, is well-described. This article will help increase the understanding of the utilization of lignin as an economical and alternative-resource material. It will also aid in the minimization of solid waste arising from lignin.
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11
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Yang C, Ma L, Wang X, Xing Y, Lü X. A Novel Polyphenol Oxidoreductase OhLac from Ochrobactrum sp. J10 for Lignin Degradation. Front Microbiol 2021; 12:694166. [PMID: 34671322 PMCID: PMC8521193 DOI: 10.3389/fmicb.2021.694166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
Identifying the enzymes involved in lignin degradation by bacteria is important in studying lignin valorization to produce renewable chemical products. In this paper, the catalytic oxidation of lignin by a novel multi-copper polyphenol oxidoreductase (OhLac) from the lignin degrader Ochrobactrum sp. J10 was explored. Following its expression, reconstitution, and purification, a recombinant enzyme OhLac was obtained. The OhLac enzyme was characterized kinetically against a range of substrates, including ABTS, guaiacol, and 2,6-DMP. Moreover, the effects of pH, temperature, and Cu2+ on OhLac activity and stability were determined. Gas chromatography-mass spectrometer (GC-MS) results indicated that the β-aryl ether lignin model compound guaiacylglycerol-β-guaiacyl ether (GGE) was oxidized by OhLac to generate guaiacol and vanillic acid. Molecular docking analysis of GGE and OhLac was then used to examine the significant amino residues and hydrogen bonding sites in the substrate–enzyme interaction. Altogether, we were able to investigate the mechanisms involved in lignin degradation. The breakdown of the lignocellulose materials wheat straw, corn stalk, and switchgrass by the recombinant OhLac was observed over 3 days, and the degradation results revealed that OhLac plays a key role in lignin degradation.
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Affiliation(s)
- Chenxian Yang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China.,College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Lingling Ma
- College of Food Science and Engineering, Northwest A&F University, Yangling, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Xin Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuqi Xing
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
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12
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Lu T, Yang Y, Feng WJ, Jin QC, Wu ZG, Jin ZH. Effect of the compound bacterial agent on microbial community of the aerobic compost of food waste. Lett Appl Microbiol 2021; 74:32-43. [PMID: 34608649 DOI: 10.1111/lam.13579] [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: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/28/2021] [Indexed: 11/28/2022]
Abstract
In our study, we used 16SrRNA and ITS to investigate the microbial community composition and the effect of compound bacterial agent on the microbial community composition in the aerobic composting process of food waste (FW). At the bacterial level, the main phyla of Group A (compost naturally) were Proteobacteria and Firmicutes, and the main species were Pseudomonas_sp._GR7, Bacillus licheniformis and Pediococcus acidilactici. The main phyla of Group B (compost with compound bacterial agent) were Proteobacteria, Firmicutes and Streptophyta, and the main species were Klebsiella pneumoniae, Cronobacter sakazakii, Macrococcus caseolyticus, Enterococcus faecalis, Citrobacter freundii and Bacillus velezensis. It is worth noting that M. caseolyticus may be able to improve the effect of odour which is an important sensory index during aerobic composting. At the fungal level, the main phylum of both Groups A and B was Ascomycota, and the main species of Group A were Paecilomyces variotii, Byssochlamys spectabilis and Aspergillus fumigatus. The main species of Group B were Ogataea polymorpha and Millerozyma farinosa. Finally, the degradation rate of Group B was 81% that was about 15% higher than that of Group A, indicating that the compound bacterial agent could effectively improve the degradation rate and the composting process, while the low abundance of the compound bacterial agent in the composting process might be due to the small initial addition or the inhibition of other bacteria or fungi in the composting process.
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Affiliation(s)
- T Lu
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China.,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Y Yang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - W J Feng
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Q C Jin
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Z G Wu
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Z H Jin
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
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13
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Li L, Wang T, Chen T, Huang W, Zhang Y, Jia R, He C. Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:128. [PMID: 34059116 PMCID: PMC8165797 DOI: 10.1186/s13068-021-01978-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/19/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H2O2 as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (Il-DyP4, corresponding to GenBank MG209114), obtained by heterologous expression, exhibits a high catalytic efficiency for phenolic compounds and a strong decolorizing ability toward various synthetic dyes. However, the enzyme structure and the catalytic residues involved in substrate oxidation remain poorly understood. RESULTS Here, we obtained a high-resolution structure (2.0 Å, PDB: 7D8M) of Il‑DyP4 with α-helices, anti-parallel β-sheets and one ferric heme cofactor sandwiched between two domains. The crystal structure of Il‑DyP4 revealed two heme access channels leading from the enzyme molecular surface to its heme region, and also showed four conserved amino acid residues forming the pocket for the conversion of hydrogen peroxide into the water molecule. In addition, we found that Trp264 and Trp380, were two important residues with different roles in Il‑DyP4, by using site-directed mutagenesis and an electron paramagnetic resonance (EPR) study. Trp264 is a noncatalytic residue that mainly is used for maintaining the normal spatial conformation of the heme region and the high-spin state of heme Fe3+ of Il‑DyP4, while Trp380 serves as the surface-exposed radical-forming residue that is closely related to the oxidation of substrates including not only bulky dyes, but also simple phenols. CONCLUSIONS This study is important for better understanding the catalytic properties of fungal DyPs and their structure-function relationships.
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Affiliation(s)
- Liuqing Li
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Tao Wang
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Taohua Chen
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Wenhan Huang
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Yinliang Zhang
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Rong Jia
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601.
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China.
| | - Chao He
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601.
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China.
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14
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Comparing Ligninolytic Capabilities of Bacterial and Fungal Dye-Decolorizing Peroxidases and Class-II Peroxidase-Catalases. Int J Mol Sci 2021; 22:ijms22052629. [PMID: 33807844 PMCID: PMC7961821 DOI: 10.3390/ijms22052629] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/27/2021] [Accepted: 02/28/2021] [Indexed: 11/17/2022] Open
Abstract
We aim to clarify the ligninolytic capabilities of dye-decolorizing peroxidases (DyPs) from bacteria and fungi, compared to fungal lignin peroxidase (LiP) and versatile peroxidase (VP). With this purpose, DyPs from Amycolatopsis sp., Thermomonospora curvata, and Auricularia auricula-judae, VP from Pleurotus eryngii, and LiP from Phanerochaete chrysosporium were produced, and their kinetic constants and reduction potentials determined. Sharp differences were found in the oxidation of nonphenolic simple (veratryl alcohol, VA) and dimeric (veratrylglycerol-β- guaiacyl ether, VGE) lignin model compounds, with LiP showing the highest catalytic efficiencies (around 15 and 200 s−1·mM−1 for VGE and VA, respectively), while the efficiency of the A. auricula-judae DyP was 1–3 orders of magnitude lower, and no activity was detected with the bacterial DyPs. VP and LiP also showed the highest reduction potential (1.28–1.33 V) in the rate-limiting step of the catalytic cycle (i.e., compound-II reduction to resting enzyme), estimated by stopped-flow measurements at the equilibrium, while the T. curvata DyP showed the lowest value (1.23 V). We conclude that, when using realistic enzyme doses, only fungal LiP and VP, and in much lower extent fungal DyP, oxidize nonphenolic aromatics and, therefore, have the capability to act on the main moiety of the native lignin macromolecule.
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15
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Bredon M, Depuydt E, Brisson L, Moulin L, Charles C, Haenn S, Moumen B, Bouchon D. Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod. Microorganisms 2021; 9:microorganisms9010148. [PMID: 33440837 PMCID: PMC7826753 DOI: 10.3390/microorganisms9010148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/27/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host’s diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the “eco-holobiont” conceptualization of macroorganisms.
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Affiliation(s)
- Marius Bredon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
| | - Elisabeth Depuydt
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
| | - Lucas Brisson
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
| | - Laurent Moulin
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l’Eau, R&D Biologie, F-94200 Ivry sur Seine, France; (L.M.); (C.C.); (S.H.)
| | - Ciriac Charles
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l’Eau, R&D Biologie, F-94200 Ivry sur Seine, France; (L.M.); (C.C.); (S.H.)
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, F-94700 Maisons-Alfort, France
| | - Sophie Haenn
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l’Eau, R&D Biologie, F-94200 Ivry sur Seine, France; (L.M.); (C.C.); (S.H.)
| | - Bouziane Moumen
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
| | - Didier Bouchon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
- Correspondence: ; Tel.: +33-(0)5-49-45-38-95; Fax: +33-(0)5-49-45-40-15
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16
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Kumar M, You S, Beiyuan J, Luo G, Gupta J, Kumar S, Singh L, Zhang S, Tsang DCW. Lignin valorization by bacterial genus Pseudomonas: State-of-the-art review and prospects. BIORESOURCE TECHNOLOGY 2021; 320:124412. [PMID: 33249259 DOI: 10.1016/j.biortech.2020.124412] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
The most prominent aromatic feedstock on Earth is lignin, however, lignin valorization is still an underrated subject. The principal preparatory strategies for lignin valorization are fragmentation and depolymerization which help in the production of fuels and chemicals. Owing to lignin's structural heterogeneity, these strategies result in product generation which requires tedious separation and purification to extract target products. The bacterial genus Pseudomonas has been dominant for its lignin valorization potency, owing to a robust enzymatic machinery that is used to funnel variable lignin derivatives into certain target products such as polyhydroxyalkanotes (PHAs) and cis, cis-muconic acid (MA). In this review, the potential of genus Pseudomonas in lignin valorization is critically reviewed along with the advanced genetic techniques and tools to ease the use of lignin/lignin-model compounds for the synthesis of bioproducts. This review also highlights the research gaps in lignin biovalorization and discuss the challenges and possibilities for future research.
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Affiliation(s)
- Manish Kumar
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Siming You
- University of Glasgow, James Watt School of Engineering, Glasgow G12 8 QQ, United Kingdom
| | - Jingzi Beiyuan
- Biochar Engineering Technology Research Center of Guangdong Province, School of Environment and Chemical Engineering, Foshan University, Foshan 528000, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sunil Kumar
- CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Lal Singh
- CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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17
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Rathour RK, Bhatia RK, Rana DS, Bhatt AK, Thakur N. Fabrication of thermostable and reusable nanobiocatalyst for dye decolourization by immobilization of lignin peroxidase on graphene oxide functionalized MnFe 2O 4 superparamagnetic nanoparticles. BIORESOURCE TECHNOLOGY 2020; 317:124020. [PMID: 32827973 DOI: 10.1016/j.biortech.2020.124020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 05/05/2023]
Abstract
In view of the potential applications of immobilized enzymes, partially purified Lignin Peroxidase (LiP) from Pseudomonas fluorescens LiP-RL5 was immobilized on Graphene Oxide functionalized MnFe2O4 nanoparticles (10 nm, synthesized by sol-gel auto-combustion) to fabricate a new hyperactive and thermostable nanobiocatalyst and thereafter characterized by using standard techniques. Immobilized LiP was quite stable at 50 °C with the half-life of 14 h and showed higher tolerance towards various metal ions and solvents than free LiP. Immobilized LiP retained 50% of enzyme activity even after nine consecutive runs. When tested against various textile dyes, the immobilized LiP was found quite effective with higher dye decolourization efficiency (up to 88%) within 1 h of incubation at 30 °C. The results of this research effort confirmed that the immobilization of LiP and fabrication of nanobiocatalyst increase the efficacy, stability, and reusability of the enzyme which could be efficiently utilized under harsh industrial conditions.
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Affiliation(s)
- Ranju Kumari Rathour
- Department of Biotechnology, Himachal Pradesh University Summer Hill, Shimla 5, India
| | - Ravi Kant Bhatia
- Department of Biotechnology, Himachal Pradesh University Summer Hill, Shimla 5, India
| | - Dilbag Singh Rana
- Department of Environment Science, Central University of Himachal Pradesh, Dharamshala, India
| | - Arvind Kumar Bhatt
- Department of Biotechnology, Himachal Pradesh University Summer Hill, Shimla 5, India
| | - Nagesh Thakur
- Department of Physics, Himachal Pradesh University Summer Hill, Shimla 5, India
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18
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Rathour RK, Sharma V, Rana N, Bhatia RK, Bhatt AK. Bioremediation of Simulated Textile Effluent by an Efficient Bio-catalyst Purified from a Novel Pseudomonas fluorescence LiP-RL5. ACTA ACUST UNITED AC 2020. [DOI: 10.2174/2212796814666200406100247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Microbial degradation of highly stable textile dyes, using lignin peroxidase,
is an eco-friendly, less expensive and much advantageous in comparison to the
chemical method.
Objective:
Biodegradation potential of lignin peroxidase (LiP), from Pseudomonas fluorescens
LiP-RL5, was enhanced after optimization and purification so as to use it as a potential
bioresource for the treatment of textile effluent.
Methods:
LiP producing bacterial isolate was primarily screened by methylene blue assay
followed by LiP assay. The standard protocol was used for purification of lignin peroxidase
and purified LiP was finally used for degradation of textile dyes.
Results:
57 bacterial isolates were screened for lignin peroxidase activity. Isolate LiP-RL5
showed maximum activity (19.8 ±0.33 %) in terms of methylene blue reduction in comparison
to others. Biochemical and molecular characterization of LiP-RL5 showed 99 % similarity
with P. fluorescens. Lignin peroxidase activity was increased by 50 % after optimization
of cultural conditions. Maximum enhancement in the activity was achieved when peptone
was used as a nitrogen source. LiP from P. fluorescens LiP-RL5 was further purified up to 2
folds. SDS-PAGE analysis revealed a single protein band of approximately 40 kDa. Enzyme
also showed high catalytic efficiency with Km= 6.94 mM and Vmax= 78.74 μmol/ml/min. Purified
enzyme was able to decolorize the simulated textile effluent up to 45.05 ±0.28 % after
40 minutes.
Conclusion:
: High catalytic efficiency of purified LiP from P. fluorescens LiP-RL5 suggests
its utility as a potential candidate for biodegradation of toxic dyes in the industrial effluent,
which could be successfully utilized for wastewater treatment at commercial level.
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Affiliation(s)
- Ranju K. Rathour
- Department of Biotechnology, Himachal Pradesh University, Gyan Path, Summer hill, Shimla- 171005, India
| | - Vaishali Sharma
- Department of Biotechnology, Himachal Pradesh University, Gyan Path, Summer hill, Shimla- 171005, India
| | - Nidhi Rana
- Department of Biotechnology, Himachal Pradesh University, Gyan Path, Summer hill, Shimla- 171005, India
| | - Ravi K. Bhatia
- Department of Biotechnology, Himachal Pradesh University, Gyan Path, Summer hill, Shimla- 171005, India
| | - Arvind K. Bhatt
- Department of Biotechnology, Himachal Pradesh University, Gyan Path, Summer hill, Shimla- 171005, India
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19
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Falade AO, Ekundayo TC. Emerging biotechnological potentials of DyP-type peroxidases in remediation of lignin wastes and phenolic pollutants: a global assessment (2007-2019). Lett Appl Microbiol 2020; 72:13-23. [PMID: 32974921 DOI: 10.1111/lam.13392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022]
Abstract
Dye decolourizing peroxidase (DyP) is an emerging biocatalyst with enormous bioremediation and biotechnological potentials. This study examined the global trend of research related to DyP through a bibliometric analysis. The search term 'dye decolourizing peroxidase' or 'DyP-type peroxidase' was used to retrieve published articles between 2007 and 2019 from the Web of Science (WoS) and Scopus databases. A total of 62 articles were published within the period, with an annual growth rate of 17·6%. The highest research output was observed in 2015, which accounted for about 13% of the total output in 12 years. Germany published the highest number of articles (n = 10, 16·1%) with a total citation of 478. However, the lowest number of published articles among the top 10 countries was observed in India and Korea (n = 2, 3·2%). Research collaboration was low (collaboration index = 4·08). In addition to dye decolourizing peroxidase(s) and DyP-type peroxidase(s) (n = 33, 53·23%), the top authors keywords and research focus included lignin and lignin degradation (n = 10, 16·1 %). More so, peroxidase (n = 59, 95·2%), amino acid sequence (n = 27, 46·8%), lignin (n = 24, 38·7%) and metabolism (n = 23, 37·1%) were highly represented in keywords-plus. The most common conceptual framework from this study include characterization, lignin degradation and environmental proteomics. Apart from the inherent efficient dye-decolourizing properties, this study showed that DyP has emerging biotechnological potentials in lignin degradation and remediation of phenolic environmental pollutants, which at the moment are under explored globally.
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Affiliation(s)
- A O Falade
- Department of Biochemistry, University of Medical Sciences, Ondo, Ondo State, Nigeria
| | - T C Ekundayo
- Department of Biological Sciences, University of Medical Sciences, Ondo, Ondo State, Nigeria
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20
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Catucci G, Valetti F, Sadeghi SJ, Gilardi G. Biochemical features of dye‐decolorizing peroxidases: Current impact on lignin degradation. Biotechnol Appl Biochem 2020; 67:751-759. [DOI: 10.1002/bab.2015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Gianluca Catucci
- Department of Life Sciences and Systems Biology University of Torino Torino 10123 Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology University of Torino Torino 10123 Italy
| | - Sheila J. Sadeghi
- Department of Life Sciences and Systems Biology University of Torino Torino 10123 Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology University of Torino Torino 10123 Italy
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21
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Gonçalves CC, Bruce T, Silva CDOG, Fillho EXF, Noronha EF, Carlquist M, Parachin NS. Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods. Front Microbiol 2020; 11:1081. [PMID: 32582068 PMCID: PMC7295907 DOI: 10.3389/fmicb.2020.01081] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 01/02/2023] Open
Abstract
Lignin is an abundant cell wall component, and it has been used mainly for generating steam and electricity. Nevertheless, lignin valorization, i.e. the conversion of lignin into high value-added fuels, chemicals, or materials, is crucial for the full implementation of cost-effective lignocellulosic biorefineries. From this perspective, rapid screening methods are crucial for time- and resource-efficient development of novel microbial strains and enzymes with applications in the lignin biorefinery. The present review gives an overview of recent developments and applications of a vast arsenal of activity and sequence-based methodologies for uncovering novel microbial strains with ligninolytic potential, novel enzymes for lignin depolymerization and for unraveling the main metabolic routes during growth on lignin. Finally, perspectives on the use of each of the presented methods and their respective advantages and disadvantages are discussed.
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Affiliation(s)
- Carolyne Caetano Gonçalves
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| | - Thiago Bruce
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| | | | | | - Eliane Ferreira Noronha
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, Lund, Sweden
| | - Nádia Skorupa Parachin
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
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22
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Ma L, Zhao Y, Meng L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Isolation of Thermostable Lignocellulosic Bacteria From Chicken Manure Compost and a M42 Family Endocellulase Cloning From Geobacillus thermodenitrificans Y7. Front Microbiol 2020; 11:281. [PMID: 32174898 PMCID: PMC7054444 DOI: 10.3389/fmicb.2020.00281] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/07/2020] [Indexed: 01/01/2023] Open
Abstract
The composting ecosystem provides a potential resource for finding new microorganisms with the capability for cellulose degradation. In the present study, Congo red method was used for the isolating of thermostable lignocellulose-degrading bacteria from chicken manure compost. A thermophilic strain named as Geobacillus thermodenitrificans Y7 with acid-resident property was successfully isolated and employed to degrade raw switchgrass at 60°C for 5 days, which resulted in the final degradation rates of cellulose, xylan, and acid-insoluble lignin as 18.64, 12.96, and 17.21%, respectively. In addition, GC-MS analysis about aromatic degradation affirm the degradation of lignin by G. thermodenitrificans Y7. Moreover, an endocellulase gene belong to M42 family was successfully cloned from G. thermodenitrificans Y7 and expressed in Escherichia coli BL21. Recombinant enzyme Cel-9 was purified by Ni-NTA column based the His-tag, and the molecular weight determined as 40.4 kDa by SDA-PAGE. The characterization of the enzyme Cel-9 indicated that the maximum enzyme activity was realized at 50°C and pH 8.6 and, Mn2+ could greatly improve the CMCase enzyme activity of Cel-9 at 10 mM, which was followed by Fe2+ and Co2+. Besides, it also found that the β-1,3-1,4, β-1,3, β-1,4, and β-1,6 glucan linkages all could be hydrolyzed by enzyme Cel-9. Finally, during the application of enzyme Cel-9 to switchgrass, the saccharification rates achieved to 1.81 ± 0.04% and 2.65 ± 0.03% for 50 and 100% crude enzyme, respectively. All these results indicated that both the strain G. thermodenitrificans Y7 and the recombinant endocellulase Cel-9 have the potential to be applied to the biomass industry.
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Affiliation(s)
- Lingling Ma
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuchun Zhao
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Limin Meng
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Xin Wang
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yanglei Yi
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuanyuan Shan
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Bianfang Liu
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuan Zhou
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Xin Lü
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
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23
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Bacterial enzymes for lignin depolymerisation: new biocatalysts for generation of renewable chemicals from biomass. Curr Opin Chem Biol 2020; 55:26-33. [PMID: 31918394 DOI: 10.1016/j.cbpa.2019.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 11/20/2022]
Abstract
The conversion of polymeric lignin from plant biomass into renewable chemicals is an important unsolved problem in the biorefinery concept. This article summarises recent developments in the discovery of bacterial enzymes for lignin degradation, our current understanding of their molecular mechanism of action, and their use to convert lignin or lignocellulose into aromatic chemicals. The review also discusses the recent developments in screening of metagenomic libraries for new biocatalysts, and the use of protein engineering to enhance lignin degradation activity.
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24
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Expression and Characterization of a Dye-Decolorizing Peroxidase from Pseudomonas Fluorescens Pf0-1. Catalysts 2019. [DOI: 10.3390/catal9050463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The consumption of dyes is increasing worldwide in line with the increase of population and demand for clothes and other colored products. However, the efficiency of dyeing processes is still poor and results in large amounts of colored effluents. It is desired to develop a portfolio of enzymes which can be used for the treatment of colored wastewaters. Herein, we used genome sequence information to discover a dye-decolorizing peroxidase (DyP) from Pseudomonas fluorescens Pf-01. Two genes putatively encoding for DyPs were identified in the respective genome and cloned for expression in Escherichia coli, of which one (PfDyP B2) could be overexpressed as a soluble protein. PfDyP B2 shows some typical features known for DyPs which includes the ability to convert dyes at the expense of hydrogen peroxide. Interestingly, t-butyl hydroperoxide could be used as an alternative substrate to hydrogen peroxide. Immobilization of PfDyP B2 in calcium-alginate beads resulted in a significant increase in stability: PfDyP B2 retains 80% of its initial activity after 2 h incubation at 50 °C, while the soluble enzyme is inactivated within minutes. PfDyP B2 was also tested with aniline and ethyl diazoacetate as substrates. Based on GC-MS analyses, 30% conversion of the starting material was achieved after 65 h at 30 °C. Importantly, this is the first report of a DyP-catalyzed insertion of a carbene into an N-H bond.
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Xu Z, Lei P, Zhai R, Wen Z, Jin M. Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:32. [PMID: 30815030 PMCID: PMC6376720 DOI: 10.1186/s13068-019-1376-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
Lignin is the most abundant aromatic substrate on Earth and its valorization technologies are still under developed. Depolymerization and fragmentation are the predominant preparatory strategies for valorization of lignin to chemicals and fuels. However, due to the structural heterogeneity of lignin, depolymerization and fragmentation typically result in diverse product species, which require extensive separation and purification procedures to obtain target products. For lignin valorization, bacterial-based systems have attracted increasing attention because of their diverse metabolisms, which can be used to funnel multiple lignin-based compounds into specific target products. Here, recent advances in lignin valorization using bacteria are critically reviewed, including lignin-degrading bacteria that are able to degrade lignin and use lignin-associated aromatics, various associated metabolic pathways, and application of bacterial cultures for lignin valorization. This review will provide insight into the recent breakthroughs and future trends of lignin valorization based on bacterial systems.
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Affiliation(s)
- Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Peng Lei
- Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing, 211111 China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
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Kumar P, Maharjan A, Jun H, Kim BS. Bioconversion of lignin and its derivatives into polyhydroxyalkanoates: Challenges and opportunities. Biotechnol Appl Biochem 2018; 66:153-162. [DOI: 10.1002/bab.1720] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/18/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Prasun Kumar
- Department of Chemical EngineeringChungbuk National University Chungbuk Republic of Korea
| | - Anoth Maharjan
- Department of Chemical EngineeringChungbuk National University Chungbuk Republic of Korea
| | - Hang‐Bae Jun
- Department of Environmental EngineeringChungbuk National University Chungbuk Republic of Korea
| | - Beom Soo Kim
- Department of Chemical EngineeringChungbuk National University Chungbuk Republic of Korea
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