1
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Li Y, Xu Y, Huang E, Kong L, Zeng Y. Efficient adsorption desulfurization via encapsulation of CeO 2 nanoparticles in hierarchical porous HKUST-1. J Colloid Interface Sci 2025; 689:137237. [PMID: 40054268 DOI: 10.1016/j.jcis.2025.03.026] [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: 11/26/2024] [Revised: 03/01/2025] [Accepted: 03/02/2025] [Indexed: 03/26/2025]
Abstract
Thiophene-like sulfides present in fuel oil release sulfur oxides (SOx) during combustion, which pose significant risks for both environmental sustainability and public health. Adsorption desulfurization (ADS) has garnered considerable attention because of its mild operating conditions, low production costs, and minimal impact on the octane number of fuels. Metal-organic frameworks used as desulfurizing adsorbents provide several advantages, including a high specific surface area and easily adjustable structures. Here, we synthesized the micro/mesoporous adsorbent CeO2@HP-HKUST-1 (CeO2@Hierarchical Porous-Hong Kong University of Science and Technology-1) through the hybridization of salicylic acid (SA) using a solvothermal method. We assessed the adsorption performance ofCeO2@HP- HKUST-1_1.5for benzothiophene and thiophene through batch and breakthrough adsorption experiments. The adsorption capacities for thiophene and benzothiophene were measured at 21.2 mg S/g and 35.3 mg S/g, respectively. Remarkably, in competitive toluene experiments, the adsorption capacity for benzothiophene remained significant at 28.9 mg S/g, due to enhanced Ce-S bonding interactions and the exposure of unsaturated metal centers of Cu. Additionally, regeneration experiments demonstrated that CeO2@HP-HKUST-1 retained excellent adsorption capacities after four cycles. These findings highlight the potential of CeO2@HP-HKUST-1 as an effective adsorbent for desulfurization applications.
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Affiliation(s)
- Yuting Li
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Yueyang Xu
- Science and Technology Research Institute, National Energy Group, Nanjing 210031, China
| | - Erjian Huang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Liming Kong
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China.
| | - Yongping Zeng
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China.
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2
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Martzoukou O, Klenias F, Kopsini E, Hatzinikolaou DG. Biodesulfurization enhancement via targeted re-insertion of the flavin reductase dszD in the genome of the model strain Rhodococcus qingshengii IGTS8. Heliyon 2025; 11:e41899. [PMID: 39897813 PMCID: PMC11783014 DOI: 10.1016/j.heliyon.2025.e41899] [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: 07/05/2024] [Revised: 01/09/2025] [Accepted: 01/10/2025] [Indexed: 02/04/2025] Open
Abstract
Biodesulfurization (BDS) has emerged as an alternative to the excessively costly hydrodesulfurization of recalcitrant heterocyclic sulfur compounds, such as dibenzothiophene (DBT) and its derivatives. The model desulfurizing strain Rhodococcus qingshengii IGTS8 is responsible for the removal of sulfur through the 4S metabolic pathway, operating through a plasmid-borne dszABC operon, as well as the chromosomal gene for the flavin reductase, d szD. However, naturally occurring biocatalysts do not exhibit the required BDS activity to be useful for industrial applications and for this reason, genetic modifications are currently being explored. Here, we constructed a genetically modified R. qingshengii IGTS8 strain, which carries an additional copy of the flavin reductase gene dszD under the control of the rhodococcal promoter P kap1 , inserted in the neutral chromosomal genetic locus crtI. We conducted a comparative study of the growth and biodesulfurization capabilities of P kap1 -dszD, wild-type and crtIΔ strains, grown on different types and concentrations of carbon and sulfur sources. A significant enhancement of biodesulfurization activity, maximum calculated biomass, and dszD transcript levels in the presence of DBT as the sole sulfur source was achieved for the P kap1 -dszD strain paving the way for further studies that could lead to a more viable commercial biodesulfurization process.
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Affiliation(s)
- Olga Martzoukou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Fotios Klenias
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleni Kopsini
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitris G. Hatzinikolaou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
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3
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Bagchi A, Srivastava P. Genetic and metabolic engineering approaches for enhanced biodesulfurization of petroleum fractions. Front Bioeng Biotechnol 2024; 12:1482270. [PMID: 39530058 PMCID: PMC11550978 DOI: 10.3389/fbioe.2024.1482270] [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: 08/18/2024] [Accepted: 10/10/2024] [Indexed: 11/16/2024] Open
Abstract
Sulfur, an abundant component of crude oil, causes severe damage to the environment, poses risks to human health, and poisons the catalysts used in combustion engines. Hydrodesulfurization, the conventionally used method, is not sufficient to remove thiophenes like dibenzothiophene (DBT) and other aromatic heterocyclic compounds. The push for "ultra-clean" fuels, with sulfur content less than 15 ppm, drives the need for deep desulfurization. Thus, in conjunction with hydrodesulfurization, efficient and eco-friendly methods of deep desulfurization, like biodesulfurization, are desirable. In biodesulfurization, naturally desulfurizing microorganisms are used, with genetic engineering and biotechnology, to reduce the sulfur content of crude oil to below 15 ppm. In this review, we describe genetic and metabolic engineering approaches reported to date to develop more efficient methods to carry out biodesulfurization, making it a practically applicable reality.
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Affiliation(s)
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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4
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Yue K, Acevedo O. Uncovering the Critical Factors that Enable Extractive Desulfurization of Fuels in Ionic Liquids and Deep Eutectic Solvents from Simulations. J Phys Chem B 2023. [PMID: 37413969 DOI: 10.1021/acs.jpcb.3c02652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Environmental regulatory agencies have implemented stringent restrictions on the permissible levels of sulfur compounds in fuel to reduce harmful emissions and improve air quality. Problematically, traditional desulfurization methods have shown low effectiveness in the removal of refractory sulfur compounds, e.g., thiophene (TS), dibenzothiophene (DBT), and 4-methyldibenzothiophene (MDBT). In this work, molecular dynamics (MD) simulations and free energy perturbation (FEP) have been applied to investigate the use of ionic liquids (ILs) and deep eutectic solvents (DESs) as efficient TS/DBT/MDBT extractants. For the IL simulations, the selected cation was 1-butyl-3-methylimidazolium [BMIM] and the anions included chloride [Cl], thiocyanate [SCN], tetrafluoroborate [BF4], hexafluorophosphate [PF6], and bis(trifluoromethylsulfonyl)amide [NTf2]. The DESs were composed of choline chloride with ethylene glycol (CCEtg) or with glycerol (CCGly). Calculation of excess chemical potentials predicted the ILs to be more promising extractants with energies lower by 1-3 kcal/mol compared to DESs. Increasing IL anion size was positively correlated to enhanced solvation of S-compounds, which was influenced by energetically dominant solute-anion interactions and favorable solute-[BMIM] π-π stacking. For the DESs, the solvent components offered a range of synergistic, yet comparatively weaker, electrostatic interactions that included hydrogen bonding and cation-π interactions. An in-depth analysis of the structure of IL and DES systems is presented, along with a discussion of the critical factors behind experimental trends of S-compound extraction efficiency.
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Affiliation(s)
- Kun Yue
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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5
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Bacterial Biological Factories Intended for the Desulfurization of Petroleum Products in Refineries. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The removal of sulfur by deep hydrodesulfurization is expensive and environmentally unfriendly. Additionally, sulfur is not separated completely from heterocyclic poly-aromatic compounds. In nature, several microorganisms (Rhodococcus erythropolis IGTS8, Gordonia sp., Bacillus sp., Mycobacterium sp., Paenibacillus sp. A11-2 etc.) have been reported to remove sulfur from petroleum fractions. All these microbes remove sulfur from recalcitrant organosulfur compounds via the 4S pathway, showing potential for some organosulfur compounds only. Activity up to 100 µM/g dry cell weights is needed to meet the current demand for desulfurization. The present review describes the desulfurization capability of various microorganisms acting on several kinds of sulfur sources. Genetic engineering approaches on Gordonia sp. and other species have revealed a variety of good substrate ranges of desulfurization, both for aliphatic and aromatic organosulfur compounds. Whole genome sequence analysis and 4S pathway inhibition by a pTeR group inhibitor have also been discussed. Now, emphasis is being placed on how to commercialize the microbes for industrial-level applications by incorporating biodesulfurization into hydrodesulfurization systems. Thus, this review summarizes the potentialities of microbes for desulfurization of petroleum. The information included in this review could be useful for researchers as well as the economical commercialization of bacteria in petroleum industries.
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6
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Karaiyan P, Chang CCH, Chan ES, Tey BT, Ramanan RN, Ooi CW. In silico screening and heterologous expression of soluble dimethyl sulfide monooxygenases of microbial origin in Escherichia coli. Appl Microbiol Biotechnol 2022; 106:4523-4537. [PMID: 35713659 PMCID: PMC9259527 DOI: 10.1007/s00253-022-12008-8] [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: 02/20/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
Abstract Sequence-based screening has been widely applied in the discovery of novel microbial enzymes. However, majority of the sequences in the genomic databases were annotated using computational approaches and lacks experimental characterization. Hence, the success in obtaining the functional biocatalysts with improved characteristics requires an efficient screening method that considers a wide array of factors. Recombinant expression of microbial enzymes is often hampered by the undesirable formation of inclusion body. Here, we present a systematic in silico screening method to identify the proteins expressible in soluble form and with the desired biological properties. The screening approach was adopted in the recombinant expression of dimethyl sulfide (DMS) monooxygenase in Escherichia coli. DMS monooxygenase, a two-component enzyme consisting of DmoA and DmoB subunits, was used as a model protein. The success rate of producing soluble and active DmoA is 71% (5 out of 7 genes). Interestingly, the soluble recombinant DmoA enzymes exhibited the NADH:FMN oxidoreductase activity in the absence of DmoB (second subunit), and the cofactor FMN, suggesting that DmoA is also an oxidoreductase. DmoA originated from Janthinobacterium sp. AD80 showed the maximum NADH oxidation activity (maximum reaction rate: 6.6 µM/min; specific activity: 133 µM/min/mg). This novel finding may allow DmoA to be used as an oxidoreductase biocatalyst for various industrial applications. The in silico gene screening methodology established from this study can increase the success rate of producing soluble and functional enzymes while avoiding the laborious trial and error involved in the screening of a large pool of genes available. Key points • A systematic gene screening method was demonstrated. • DmoA is also an oxidoreductase capable of oxidizing NADH and reducing FMN. • DmoA oxidizes NADH in the absence of external FMN. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12008-8.
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Affiliation(s)
- Prasanth Karaiyan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Catherine Ching Han Chang
- Arkema Thiochemicals Sdn. Bhd., Jalan PJU 1A/7A OASIS Ara Damansara, 47301, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Eng-Seng Chan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Beng Ti Tey
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.,Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. .,Arkema Thiochemicals Sdn. Bhd., Jalan PJU 1A/7A OASIS Ara Damansara, 47301, Petaling Jaya, Selangor Darul Ehsan, Malaysia.
| | - Chien Wei Ooi
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. .,Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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7
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Keshav A, Murarka P, Srivastava P. Bending is required for activation of dsz operon by the TetR family protein (DszGR). Gene 2022; 810:146061. [PMID: 34774682 DOI: 10.1016/j.gene.2021.146061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/11/2021] [Accepted: 10/26/2021] [Indexed: 11/24/2022]
Abstract
The dsz operon responsible for the biodesulfurization of organosulfurs is under the control of a 385 bp long promoter. Recently, a TetR family protein was identified which served as an activator of operon. Here we report that the TetR family protein (WP_058249973.1), named DszGR can specifically activate the dsz operon. Direct binding of the DszGR to DNA was observed at single molecule level by AFM. It was found that the binding of DszGR to the promoter DNA induces a bend by about ∼40-50° degrees which may not be enough for the activation of the promoter. Thus, bendability in the promoter sequence was analyzed. The results show that the promoter has a curvature at around -235 and -200 bp with respect to dszA start codon. On mutating this region, a decrease in activity of the promoter was observed. Our results suggest that the DszGR protein binds to the upstream sequences and induces a bend, which is facilitated by further bending of the DNA which is required for dsz promoter activity. IHF binding site present in the promoter, and a significant reduction in desulphurization activity in the absence of either IHF subunits, suggested role of IHF in regulation of the dsz operon.
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Affiliation(s)
- Aditi Keshav
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pooja Murarka
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Preeti Srivastava
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.
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8
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Desai K, Dharaskar S, Khalid M, Gedam V. Effectiveness of ionic liquids in extractive–oxidative desulfurization of liquid fuels: a review. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-021-02038-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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9
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Sar T, Chen Y, Bai Y, Liu B, Agarwal P, Stark BC, Akbas MY. Combining co-culturing of Paenibacillus strains and Vitreoscilla hemoglobin expression as a strategy to improve biodesulfurization. Lett Appl Microbiol 2021; 72:484-494. [PMID: 33305461 DOI: 10.1111/lam.13440] [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: 06/23/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 01/31/2023]
Abstract
Enhancement of the desulfurization activities of Paenibacillus strains 32O-W and 32O-Y were investigated using dibenzothiophene (DBT) and DBT sulfone (DBTS) as sources of sulphur in growth experiments. Strains 32O-W, 32O-Y and their co-culture (32O-W plus 32O-Y), and Vitreoscilla hemoglobin (VHb) expressing recombinant strain 32O-Yvgb and its co-culture with strain 32O-W were grown at varying concentrations (0·1-2 mmol l-1 ) of DBT or DBTS for 96 h, and desulfurization measured by production of 2-hydroxybiphenyl (2-HBP) and disappearance of DBT or DBTS. Of the four cultures grown with DBT as sulphur source, the best growth occurred for the 32O-Yvgb plus 32O-W co-culture at 0·1 and 0·5 mmol l-1 DBT. Although the presence of vgb provided no consistent advantage regarding growth on DBTS, strain 32O-W, as predicted by previous work, was shown to contain a partial 4S desulfurization pathway allowing it to metabolize this 4S pathway intermediate.
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Affiliation(s)
- T Sar
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze-Kocaeli, 41400, Turkey
| | - Y Chen
- Department of Biology, Illinois Institute of Technology, Chicago, IL.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL
| | - Y Bai
- Department of Biology, Illinois Institute of Technology, Chicago, IL
| | - B Liu
- Department of Biology, Illinois Institute of Technology, Chicago, IL.,Plant Pathology Laboratory, Ball Horticultural Company, West Chicago, IL
| | - P Agarwal
- Department of Biology, Illinois Institute of Technology, Chicago, IL.,Department of Psychiatry, Rush University, Chicago, IL
| | - B C Stark
- Department of Biology, Illinois Institute of Technology, Chicago, IL
| | - M Y Akbas
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze-Kocaeli, 41400, Turkey
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10
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Ito K, Takagi K, Kataoka R, Kiyota H. Biochemical characterization of NADH:FMN oxidoreductase HcbA3 from Nocardioides sp. PD653 in catalyzing aerobic HCB dechlorination. JOURNAL OF PESTICIDE SCIENCE 2020; 45:125-131. [PMID: 32913414 PMCID: PMC7453296 DOI: 10.1584/jpestics.d20-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Nocardioides sp. PD653 genes hcbA1, hcbA2, and hcbA3 encode enzymes that catalyze the oxidative dehalogenation of hexachlorobenzene (HCB), which is one of the most recalcitrant persistent organic pollutants (POPs). In this study, HcbA1, HcbA2, and HcbA3 were heterologously expressed and characterized. Among the flavin species tested, HcbA3 showed the highest affinity for FMN with a K d value of 0.75±0.17 µM. Kinetic assays revealed that HcbA3 followed a ping-pong bi-bi mechanism for the reduction of flavins. The K m for NADH and FMN was 51.66±11.58 µM and 4.43±0.69 µM, respectively. For both NADH and FMN, the V max and k cat were 2.21±0.86 µM and 66.74±5.91 sec-1, respectively. We also successfully reconstituted the oxidative dehalogenase reaction in vitro, which consisted of HcbA1, HcbA3, FMN, and NADH, suggesting that HcbA3 may be the partner reductase component for HcbA1 in Nocardioides sp. PD653.
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Affiliation(s)
- Koji Ito
- Hazardous Chemical Division, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organisation, Kannondai, Tsukuba-city, Ibaraki, Japan
| | - Kazuhiro Takagi
- Hazardous Chemical Division, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organisation, Kannondai, Tsukuba-city, Ibaraki, Japan
| | - Ryota Kataoka
- Department of Environmental Sciences, University of Yamanashi, Kofu-city, Yamanashi, Japan
| | - Hiromasa Kiyota
- Graduate School of Environmental and Life Science, Okayama University, Tsushima, Okayama-city, Okayama, Japan
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11
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Sousa JPM, Neves RPP, Sousa SF, Ramos MJ, Fernandes PA. Reaction Mechanism and Determinants for Efficient Catalysis by DszB, a Key Enzyme for Crude Oil Bio-desulfurization. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03122] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- João P. M. Sousa
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Maria J. Ramos
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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12
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Parveen S, Akhtar N, Ghauri MA, Akhtar K. Conventional genetic manipulation of desulfurizing bacteria and prospects of using CRISPR-Cas systems for enhanced desulfurization activity. Crit Rev Microbiol 2020; 46:300-320. [PMID: 32530374 DOI: 10.1080/1040841x.2020.1772195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Highly active and stable biocatalysts are the prerequisite for industrial scale application of the biodesulfurization process. Scientists are making efforts for increasing the desulfurizing activity of native strains by employing various genetic engineering approaches. Nevertheless, the achieved desulfurization rate is lower than the industrial requirements. Thus, there is a dire need to use efficient genetic tools for precise genome editing of desulfurizing bacteria for enhanced efficiency. In comparison to the previously used genetic engineering tools the newly developed CRISPR-Cas is a more efficient and simple genetic tool that has been successfully applied for targeted genome modification of eukaryotes as well as prokaryotes. In this paper, we have reviewed the approaches, previously used to enhance the biodesulfurization rates of the sulfur metabolizing microorganisms and have discussed the potential of CRISPR-Cas systems in engineering desulfurizing biocatalysts. We have also proposed a model to construct competent desulfurizing recombinants involving use of CRISPR-Cas technology. The model can be used to over-express the dsz genes under a constitutive promoter in a suitable heterologous host, to get a steady expression of desulfurization pathway. This may serve as an inducement to develop better performing desulfurizing recombinant strains using CRISPR-Cas systems, which can be helpful in increasing the rate of biodesulfurization in future.
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Affiliation(s)
- Sana Parveen
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad A Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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13
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Jha D, Haider MB, Kumar R, Byamba-Ochir N, Shim WG, Marriyappan Sivagnanam B, Moon H. Enhanced Adsorptive Desulfurization Using Mongolian Anthracite-Based Activated Carbon. ACS OMEGA 2019; 4:20844-20853. [PMID: 31970308 PMCID: PMC6972957 DOI: 10.1021/acsomega.9b03432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
This study reports usage of Mongolian anthracite-based porous activated carbons (PMACs), namely, PMAC 1/3 and PMAC 1/4 for model diesel fuel desulfurization, having 500 ppmw of dibenzothiophene (DBT) in n-heptane. Further, the effects of contact time, adsorbent dosage, and temperature on the adsorption capacity were studied systematically. The experimental adsorption isotherm results were well represented by the Sips isotherm for PMAC 1/3 and the dual site Langmuir isotherm for PMAC 1/4. The maximum DBT adsorption by PMAC 1/3 and PMAC 1/4 were 99.7 and 95.7%, respectively. The kinetics for the adsorption of DBT on PMACs follows the pseudo second order behavior. The Weber-Morris plot shows the multilinearity over the entire time range, suggesting that both the surface and pore diffusions control the adsorption. The values of boundary layer thickness for PMAC 1/4 and PMAC 1/3 were found to be 3.183 and 1.643, respectively. Thus, PMAC 1/4 possesses more surface diffusion control than PMAC 1/3. The changes in Gibbs free energy (ΔG°), entropy (ΔS°), and enthalpy (ΔH°) are negative, which confirms that the studied process is spontaneous and exothermic and possesses less randomness at the interface. Based on the Sips isotherm, single-stage batch-adsorber design was prepared for the adsorption of DBT onto PMAC 1/3.
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Affiliation(s)
- Divyam Jha
- Department of Chemical Engineering, Rajiv
Gandhi Institute of Petroleum Technology, Jais 229304,
India
| | - Mohd Belal Haider
- Department of Chemical Engineering, Rajiv
Gandhi Institute of Petroleum Technology, Jais 229304,
India
| | - Rakesh Kumar
- Department of Chemical Engineering, Rajiv
Gandhi Institute of Petroleum Technology, Jais 229304,
India
| | - Narandalai Byamba-Ochir
- Institute of Chemistry and Chemical Technology,
Mongolian Academy of Sciences, Peace Avenue, Ulaanbaatar
13330, Mongolia
| | - Wang Geun Shim
- Department of Polymer Science and Engineering,
Sunchon National University, Suncheon-si, Jeollanam-do 57922,
Republic of Korea
| | | | - Hee Moon
- School of Chemical Engineering, Chonnam
National University, 77 Yongbong-Ro, Buk-Gu, Gwangju 61186,
Republic of Korea
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14
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Yu Y, Mills LC, Englert DL, Payne CM. Inhibition Mechanisms of Rhodococcus Erythropolis 2′-Hydroxybiphenyl-2-sulfinate Desulfinase (DszB). J Phys Chem B 2019; 123:9054-9065. [DOI: 10.1021/acs.jpcb.9b05252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yue Yu
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, United States
| | - Landon C. Mills
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, United States
| | - Derek L. Englert
- Department of Chemical and Materials Engineering, University of Kentucky, Paducah, Kentucky, United States
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, United States
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15
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Gun G, Imamoglu R, Tatli O, Yurum Y, Tarik Baykal A, Dinler-Doganay G. Hyperthermophilic flavin reductase from Sulfolobus solfataricus P2: Production and biochemical characterization. Biotechnol Appl Biochem 2019; 66:915-923. [PMID: 31396993 DOI: 10.1002/bab.1801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/03/2019] [Indexed: 11/11/2022]
Abstract
Nicotinamide adenine dinucleotide phosphate (NAD(P)H)-flavin oxidoreductases (flavin reductases) catalyze the reduction of flavin by NAD(P)H and provide the reduced form of flavin mononucleotide (FMN) to flavin-dependent monooxygenases. Based on bioinformatics analysis, we identified a putative flavin reductase gene, sso2055, in the genome of hyperthermophilic archaeon Sulfolobus solfataricus P2, and further cloned this target sequence into an expression vector. The cloned flavin reductase (EC. 1.5.1.30) was purified to homogeneity and characterized further. The purified enzyme exists as a monomer of 17.8 kDa, free of chromogenic cofactors. Homology modeling revealed this enzyme as a TIM barrel, which is also supported by circular dichroism measurements revealing a beta-sheet rich content. The optimal pH for SSO2055 activity was pH 6.5 in phosphate buffer and the highest activity observed was at 120 °C within the measurable temperature. We showed that this enzyme can use FMN and flavin adenine dinucleotide (FAD) as a substrate to generate their reduced forms. The purified enzyme is predicted to be a potential flavin reductase of flavin-dependent monooxygenases that could be involved in the biodesulfurization process of S. solfataricus P2.
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Affiliation(s)
- Gokhan Gun
- Department of Molecular Biology & Genetics, Istanbul Technical University, Maslak, Istanbul, Turkey
| | - Rahmi Imamoglu
- Department of Molecular Biology & Genetics, Istanbul Technical University, Maslak, Istanbul, Turkey
| | - Ozge Tatli
- Department of Molecular Biology & Genetics, Istanbul Technical University, Maslak, Istanbul, Turkey.,Department of Molecular Biology & Genetics, Istanbul Medeniyet University, Istanbul, Turkey
| | - Yuda Yurum
- Department of Molecular Biology & Genetics, Sabanci University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, School of Medicine, Acibadem University, Istanbul, Turkey
| | - Gizem Dinler-Doganay
- Department of Molecular Biology & Genetics, Istanbul Technical University, Maslak, Istanbul, Turkey
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16
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Li L, Shen X, Zhao C, Liu Q, Liu X, Wu Y. Biodegradation of dibenzothiophene by efficient Pseudomonas sp. LKY-5 with the production of a biosurfactant. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:50-57. [PMID: 30921696 DOI: 10.1016/j.ecoenv.2019.03.070] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/16/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
A potent bacterial strain capable of degrading dibenzothiophene (DBT) was isolated and evaluated for its characteristics. The strain, designated as LKY-5, is rod-shaped, gram-negative, and occurs mainly in clusters. It was identified as belonging to the Pseudomonas genus based on the 16S rDNA sequence and phylogenic analysis. Determination of its DBT depletion efficiency by gas chromatography revealed that the isolate was able to completely degrade up to 100 mg L-1 DBT within 144 h. The pH values, DBT concentrations, and biomasses in the medium varied significantly in the initial 24 h. A biosurfactant produced by LKY-5 was extracted and identified as a di-rhamnolipid with the formula Rha-Rha-C8-C8:1 by HPLC-ESI-MS/MS. There were 26 metabolites in the DBT degradation process. Pseudomonas sp. LKY-5 exhibited unusually high DBT degradation efficiency via multiple metabolic pathways. Compared with the reported 4S and Kodama pathways, two more expanded metabolic pathways for the degradation of DBT are proposed. The polycyclic aromatic sulfur heterocycles (PASHs) in diesel, such as C1-DBT, C2-DBT, C3-DBT, 4,6-DMDBT, and 2,4,6-TMDBT, can also be degraded with 28.2-42.3% efficiency. The results showed that LKY-5 is an excellent bacterial candidate for the bioremediation of PASH-contaminated sites and sediments.
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Affiliation(s)
- Lin Li
- State Key Laboratory of Petroleum Pollution Control, Beijing, 102206, PR China; College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong, 266590, China.
| | - Xianwei Shen
- Qingdao Dongjiakou Economic Zone Management Committee, Qingdao, Shandong, 266409, China
| | - Chaocheng Zhao
- College of Chemical Engineering, China University of Petroleum (East China), No. 66, Changjiang West Road, Huangdao District, Qingdao, PR China.
| | - Qiyou Liu
- College of Chemical Engineering, China University of Petroleum (East China), No. 66, Changjiang West Road, Huangdao District, Qingdao, PR China
| | - Xuwei Liu
- College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong, 266590, China
| | - Yanan Wu
- College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong, 266590, China
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17
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Sikarwar P, Gosu V, Subbaramaiah V. An overview of conventional and alternative technologies for the production of ultra-low-sulfur fuels. REV CHEM ENG 2019. [DOI: 10.1515/revce-2017-0082] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Environmental concerns have given a great deal of attention for the production of ultra-low-sulfur fuels. The conventional hydrodesulfurization (HDS) process has high operating cost and also encounters difficulty in removing sulfur compound with steric hindrance. Consequently, various research efforts have been made to overcome the limitation of conventional HDS process and exploring the alternative technologies for deep desulfurization. The alternative processes being explored for the production of ultra-low-sulfur content fuel are adsorptive desulfurization (ADS), biodesulfurization (BDS), oxidative desulfurization (ODS), and extractive desulfurization (EDS). The present article provided the comprehensive information on the basic principle, reaction mechanism, workability, advantages, and disadvantages of conventional and alternative technologies. This review article aims to provide valuable insight into the recent advances made in conventional HDS process and alternative techniques. For deep desulfurization of liquid fuels, integration of conventional HDS with an alternative technique is also proposed.
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18
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Anteneh YS, Franco CMM. Whole Cell Actinobacteria as Biocatalysts. Front Microbiol 2019; 10:77. [PMID: 30833932 PMCID: PMC6387938 DOI: 10.3389/fmicb.2019.00077] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/15/2019] [Indexed: 12/25/2022] Open
Abstract
Production of fuels, therapeutic drugs, chemicals, and biomaterials using sustainable biological processes have received renewed attention due to increasing environmental concerns. Despite having high industrial output, most of the current chemical processes are associated with environmentally undesirable by-products which escalate the cost of downstream processing. Compared to chemical processes, whole cell biocatalysts offer several advantages including high selectivity, catalytic efficiency, milder operational conditions and low impact on the environment, making this approach the current choice for synthesis and manufacturing of different industrial products. In this review, we present the application of whole cell actinobacteria for the synthesis of biologically active compounds, biofuel production and conversion of harmful compounds to less toxic by-products. Actinobacteria alone are responsible for the production of nearly half of the documented biologically active metabolites and many enzymes; with the involvement of various species of whole cell actinobacteria such as Rhodococcus, Streptomyces, Nocardia and Corynebacterium for the production of useful industrial commodities.
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Affiliation(s)
- Yitayal Shiferaw Anteneh
- College of Medicine and Public Health, Medical Biotechnology, Flinders University, Bedford Park, SA, Australia
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
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19
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Willetts A. Characterised Flavin-Dependent Two-Component Monooxygenases from the CAM Plasmid of Pseudomonas putida ATCC 17453 (NCIMB 10007): ketolactonases by Another Name. Microorganisms 2018; 7:E1. [PMID: 30577535 PMCID: PMC6352141 DOI: 10.3390/microorganisms7010001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 11/17/2022] Open
Abstract
The CAM plasmid-coded isoenzymic diketocamphane monooxygenases induced in Pseudomonas putida ATCC 17453 (NCIMB 10007) by growth of the bacterium on the bicyclic monoterpene (rac)-camphor are notable both for their interesting history, and their strategic importance in chemoenzymatic syntheses. Originally named 'ketolactonase-an enzyme system for cyclic lactonization' because of its characterised mode of action, (+)-camphor-induced 2,5-diketocamphane 1,2-monooxygenase was the first example of a Baeyer-Villiger monooxygenase activity to be confirmed in vitro. Both this enzyme and the enantiocomplementary (-)-camphor-induced 3,6-diketocamphane 1,6-monooxygenase were mistakenly classified and studied as coenzyme-containing flavoproteins for nearly 40 years before being correctly recognised and reinvestigated as FMN-dependent two-component monooxygenases. As has subsequently become evident, both the nature and number of flavin reductases able to supply the requisite reduced flavin co-substrate for the monooxygenases changes progressively throughout the different phases of camphor-dependent growth. Highly purified preparations of the enantiocomplementary monooxygenases have been exploited successfully for undertaking both nucleophilic and electrophilic biooxidations generating various enantiopure lactones and sulfoxides of value as chiral synthons and auxiliaries, respectively. In this review the chequered history, current functional understanding, and scope and value as biocatalysts of the diketocamphane monooxygenases are discussed.
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Affiliation(s)
- Andrew Willetts
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, UK.
- Curnow Consultancies, Helston TR13 9PQ, UK.
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20
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Barbosa ACC, Neves RPP, Sousa SF, Ramos MJ, Fernandes PA. Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana C. C. Barbosa
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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21
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Su T, Su J, Liu S, Zhang C, He J, Huang Y, Xu S, Gu L. Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the "4S" Desulfurization Pathway. Front Microbiol 2018; 9:231. [PMID: 29497411 PMCID: PMC5819316 DOI: 10.3389/fmicb.2018.00231] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/30/2018] [Indexed: 11/13/2022] Open
Abstract
Dibenzothiophene (DBT) and their derivatives, accounting for the major part of the sulfur components in crude oil, make one of the most significant pollution sources. The DBT sulfone monooxygenase BdsA, one of the key enzymes in the “4S” desulfurization pathway, catalyzes the oxidation of DBT sulfone to 2′-hydroxybiphenyl 2-sulfonic acid (HBPSi). Here, we determined the crystal structure of BdsA from Bacillus subtilis WU-S2B, at the resolution of 2.2 Å, and the structure of the BdsA-FMN complex at 2.4 Å. BdsA and the BdsA-FMN complex exist as tetramers. DBT sulfone was placed into the active site by molecular docking. Seven residues (Phe12, His20, Phe56, Phe246, Val248, His316, and Val372) are found to be involved in the binding of DBT sulfone. The importance of these residues is supported by the study of the catalytic activity of the active site variants. Structural analysis and enzyme activity assay confirmed the importance of the right position and orientation of FMN and DBT sulfone, as well as the involvement of Ser139 as a nucleophile in catalysis. This work combined with our previous structure of DszC provides a systematic structural basis for the development of engineered desulfurization enzymes with higher efficiency and stability.
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Affiliation(s)
- Tiantian Su
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Jing Su
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China.,Faculty of Light Industry, Province Key Laboratory of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shiheng Liu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Conggang Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Jing He
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Yan Huang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
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22
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Ferreira P, Sousa SF, Fernandes PA, Ramos MJ. Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives. Chemistry 2017; 23:17231-17241. [PMID: 28976031 DOI: 10.1002/chem.201704057] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Indexed: 12/18/2022]
Abstract
The enhancement of the catalytic power of enzymes is a subject of enormous interest both for science and for industry. The latter, in particular, due to the vast applications enzymes can have in industrial processes, for instance in the desulfurization of crude oil, which is mandatory by law in many developed countries and is currently performed using costly chemical processes. In this work we sought to enhance the turnover rate of DszD from Rhodococcus erythropolis, a NADH-FMN oxidoreductase responsible for supplying FMNH2 to DszA and DszC in the biodesulfurization process of crude oil, the 4S pathway. For this purpose, we replaced the wild type spectator residue of the rate limiting step of the reduction of FMN to FMNH2 , a process catalysed by DszD and known to play an important role in the reaction energy profile. As replacements, we used all the naturally occurring amino acids, one at a time, using computational methodologies, and repeated the above-mentioned reaction with each mutant. To calculate the different free energy profiles, one for each mutated model, we applied quantum mechanics/molecular mechanics (QM/MM) methods within an ONIOM scheme. The free energy barriers obtained varied between 15.1 and 29.9 kcal mol-1 . Multiple factors contributed to the different ΔG values. The most relevant were electrostatic interactions and the induction of a favourable alignment between substrate and cofactor. These results confirm the great potential that chirurgic mutations have for increasing the catalytic power of DszD in relation to the wild type (wt) enzyme.
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Affiliation(s)
- Pedro Ferreira
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria João Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
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23
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Martínez I, El-Said Mohamed M, Santos VE, García JL, García-Ochoa F, Díaz E. Metabolic and process engineering for biodesulfurization in Gram-negative bacteria. J Biotechnol 2017; 262:47-55. [PMID: 28947364 DOI: 10.1016/j.jbiotec.2017.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 11/19/2022]
Abstract
Microbial desulfurization or biodesulfurization (BDS) is an attractive low-cost and environmentally friendly complementary technology to the hydrotreating chemical process based on the potential of certain bacteria to specifically remove sulfur from S-heterocyclic compounds of crude fuels that are recalcitrant to the chemical treatments. The 4S or Dsz sulfur specific pathway for dibenzothiophene (DBT) and alkyl-substituted DBTs, widely used as model S-heterocyclic compounds, has been extensively studied at the physiological, biochemical and genetic levels mainly in Gram-positive bacteria. Nevertheless, several Gram-negative bacteria have been also used in BDS because they are endowed with some properties, e.g., broad metabolic versatility and easy genetic and genomic manipulation, that make them suitable chassis for systems metabolic engineering strategies. A high number of recombinant bacteria, many of which are Pseudomonas strains, have been constructed to overcome the major bottlenecks of the desulfurization process, i.e., expression of the dsz operon, activity of the Dsz enzymes, retro-inhibition of the Dsz pathway, availability of reducing power, uptake-secretion of substrate and intermediates, tolerance to organic solvents and metals, and other host-specific limitations. However, to attain a BDS process with industrial applicability, it is necessary to apply all the knowledge and advances achieved at the genetic and metabolic levels to the process engineering level, i.e., kinetic modelling, scale-up of biphasic systems, enhancing mass transfer rates, biocatalyst separation, etc. The production of high-added value products derived from the organosulfur material present in oil can be regarded also as an economically viable process that has barely begun to be explored.
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Affiliation(s)
- I Martínez
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain
| | - M El-Said Mohamed
- Research and Development Center, Saudi Aramco, Dhahran, Saudi Arabia
| | - V E Santos
- Chemical Engineering Department, Complutense University of Madrid, 28040 Madrid Spain
| | - J L García
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain; Institute for Integrative Systems Biology (I2SysBio) (University of Valencia-CSIC), 46980 Paterna Valencia, Spain
| | - F García-Ochoa
- Chemical Engineering Department, Complutense University of Madrid, 28040 Madrid Spain
| | - E Díaz
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain.
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24
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Hino T, Hamamoto H, Suzuki H, Yagi H, Ohshiro T, Nagano S. Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity. J Biol Chem 2017; 292:15804-15813. [PMID: 28768765 DOI: 10.1074/jbc.m117.788513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/23/2017] [Indexed: 11/06/2022] Open
Abstract
Sulfur compounds in fossil fuels are a major source of environmental pollution, and microbial desulfurization has emerged as a promising technology for removing sulfur under mild conditions. The enzyme TdsC from the thermophile Paenibacillus sp. A11-2 is a two-component flavin-dependent monooxygenase that catalyzes the oxygenation of dibenzothiophene (DBT) to its sulfoxide (DBTO) and sulfone (DBTO2) during microbial desulfurization. The crystal structures of the apo and flavin mononucleotide (FMN)-bound forms of DszC, an ortholog of TdsC, were previously determined, although the structure of the ternary substrate-FMN-enzyme complex remains unknown. Herein, we report the crystal structures of the DBT-FMN-TdsC and DBTO-FMN-TdsC complexes. These ternary structures revealed many hydrophobic and hydrogen-bonding interactions with the substrate, and the position of the substrate could reasonably explain the two-step oxygenation of DBT by TdsC. We also determined the crystal structure of the indole-bound enzyme because TdsC, but not DszC, can also oxidize indole, and we observed that indole binding did not induce global conformational changes in TdsC with or without bound FMN. We also found that the two loop regions close to the FMN-binding site are disordered in apo-TdsC and become structured upon FMN binding. Alanine substitutions of Tyr-93 and His-388, which are located close to the substrate and FMN bound to TdsC, significantly decreased benzothiophene oxygenation activity, suggesting their involvement in supplying protons to the active site. Interestingly, these substitutions increased DBT oxygenation activity by TdsC, indicating that expanding the substrate-binding site can increase the oxygenation activity of TdsC on larger sulfur-containing substrates, a property that should prove useful for future microbial desulfurization applications.
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Affiliation(s)
- Tomoya Hino
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori 680-8552, Japan
| | - Haruka Hamamoto
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori 680-8552, Japan
| | - Hirokazu Suzuki
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori 680-8552, Japan
| | - Hisashi Yagi
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori 680-8552, Japan
| | - Takashi Ohshiro
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori 680-8552, Japan
| | - Shingo Nagano
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori 680-8552, Japan
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25
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Geronimo I, Nigam SR, Payne CM. Desulfination by 2'-hydroxybiphenyl-2-sulfinate desulfinase proceeds via electrophilic aromatic substitution by the cysteine-27 proton. Chem Sci 2017; 8:5078-5086. [PMID: 30155223 PMCID: PMC6100217 DOI: 10.1039/c7sc00496f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/15/2017] [Indexed: 12/02/2022] Open
Abstract
Density functional theory shows that the rate-limiting desulfination step in biodesulfurization involves concerted electrophilic substitution with the Cys-27 proton.
Biodesulfurization is an attractive option for enzymatically removing sulfur from the recalcitrant thiophenic derivatives that comprise the majority of organosulfur compounds remaining in hydrotreated petroleum products. Desulfurization in the bacteria Rhodococcus erythropolis follows a four-step pathway culminating in C–S bond cleavage in the 2′-hydroxybiphenyl-2-sulfinate (HBPS) intermediate to yield 2-hydroxybiphenyl and bisulfite. The reaction, catalyzed by 2′-hydroxybiphenyl-2-sulfinate desulfinase (DszB), is the rate-limiting step and also the least understood, as experimental evidence points to a mechanism unlike that of other desulfinases. On the basis of structural and biochemical evidence, two possible mechanisms have been proposed: nucleophilic addition and electrophilic aromatic substitution. Density functional theory calculations showed that electrophilic substitution by a proton is the lower energy pathway and is consistent with previous kinetic and site-directed mutagenesis studies. C27 transfers its proton to HBPS, leading directly to the release of SO2 without the formation of a carbocation intermediate. The H60–S25 dyad stabilizes the transition state by withdrawing the developing negative charge on cysteine. Establishing the desulfination mechanism and specific role of active site residues, accomplished in this study, is essential to protein engineering efforts to increase DszB catalytic activity, which is currently too low for industrial-scale application.
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Affiliation(s)
- Inacrist Geronimo
- Department of Chemical and Materials Engineering , University of Kentucky , Lexington , Kentucky 40506-0046 , USA .
| | - Shawn R Nigam
- Department of Chemical and Materials Engineering , University of Kentucky , Lexington , Kentucky 40506-0046 , USA .
| | - Christina M Payne
- Department of Chemical and Materials Engineering , University of Kentucky , Lexington , Kentucky 40506-0046 , USA .
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26
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Yu Y, Fursule IA, Mills LC, Englert DL, Berron BJ, Payne CM. CHARMM force field parameters for 2′-hydroxybiphenyl-2-sulfinate, 2-hydroxybiphenyl, and related analogs. J Mol Graph Model 2017; 72:32-42. [DOI: 10.1016/j.jmgm.2016.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 11/26/2022]
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27
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Wang J, Butler RR, Wu F, Pombert JF, Kilbane JJ, Stark BC. Enhancement of Microbial Biodesulfurization via Genetic Engineering and Adaptive Evolution. PLoS One 2017; 12:e0168833. [PMID: 28060828 PMCID: PMC5218467 DOI: 10.1371/journal.pone.0168833] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/07/2016] [Indexed: 11/19/2022] Open
Abstract
In previous work from our laboratories a synthetic gene encoding a peptide (“Sulpeptide 1” or “S1”) with a high proportion of methionine and cysteine residues had been designed to act as a sulfur sink and was inserted into the dsz (desulfurization) operon of Rhodococcus erythropolis IGTS8. In the work described here this construct (dszAS1BC) and the intact dsz operon (dszABC) cloned into vector pRESX under control of the (Rhodococcus) kstD promoter were transformed into the desulfurization-negative strain CW25 of Rhodococcus qingshengii. The resulting strains (CW25[pRESX-dszABC] and CW25[pRESX-dszAS1BC]) were subjected to adaptive selection by repeated passages at log phase (up to 100 times) in minimal medium with dibenzothiophene (DBT) as sole sulfur source. For both strains DBT metabolism peaked early in the selection process and then decreased, eventually averaging four times that of the initial transformed cells; the maximum specific activity achieved by CW25[pRESX-dszAS1BC] exceeded that of CW25[pRESX-dszABC]. Growth rates increased by 7-fold (CW25[pRESX-dszABC]) and 13-fold (CW25[pRESX-dszAS1BC]) and these increases were stable. The adaptations of CW25[pRESX-dszAS1BC] were correlated with a 3-5X increase in plasmid copy numbers from those of the initial transformed cells; whole genome sequencing indicated that during its selection processes no mutations occurred to any of the dsz, S1, or other genes and promoters involved in sulfur metabolism, stress response, or DNA methylation, and that the effect of the sulfur sink produced by S1 is likely very small compared to the cells’ overall cysteine and methionine requirements. Nevertheless, a combination of genetic engineering using sulfur sinks and increasing Dsz capability with adaptive selection may be a viable strategy to increase biodesulfurization ability.
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Affiliation(s)
- Jia Wang
- Department of Biology, Illinois Institute of Technology, Chicago IL, United States of America
| | - Robert R. Butler
- Department of Biology, Illinois Institute of Technology, Chicago IL, United States of America
| | - Fan Wu
- Department of Biology, Illinois Institute of Technology, Chicago IL, United States of America
| | - Jean-François Pombert
- Department of Biology, Illinois Institute of Technology, Chicago IL, United States of America
| | - John J. Kilbane
- Department of Biology, Illinois Institute of Technology, Chicago IL, United States of America
| | - Benjamin C. Stark
- Department of Biology, Illinois Institute of Technology, Chicago IL, United States of America
- * E-mail:
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Sousa SF, Sousa JFM, Barbosa ACC, Ferreira CE, Neves RPP, Ribeiro AJM, Fernandes PA, Ramos MJ. Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD). J Phys Chem A 2016; 120:5300-6. [DOI: 10.1021/acs.jpca.6b01536] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sérgio F. Sousa
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Joana F. M. Sousa
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Ana C. C. Barbosa
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Cleide E. Ferreira
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - António J. M. Ribeiro
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria João Ramos
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Martínez I, Mohamed MES, Rozas D, García JL, Díaz E. Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds. Metab Eng 2016; 35:46-54. [PMID: 26802977 DOI: 10.1016/j.ymben.2016.01.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/27/2015] [Accepted: 01/11/2016] [Indexed: 01/04/2023]
Abstract
The 4S pathway is the most studied bioprocess for the removal of the recalcitrant sulfur of aromatic heterocycles present in fuels. It consists of three sequential functional units, encoded by the dszABCD genes, through which the model compound dibenzothiophene (DBT) is transformed into the sulfur-free 2-hydroxybiphenyl (2HBP) molecule. In this work, a set of synthetic dsz cassettes were implanted in Pseudomonas putida KT2440, a model bacterial "chassis" for metabolic engineering studies. The complete dszB1A1C1-D1 cassette behaved as an attractive alternative - to the previously constructed recombinant dsz cassettes - for the conversion of DBT into 2HBP. Refactoring the 4S pathway by the use of synthetic dsz modules encoding individual 4S pathway reactions revealed unanticipated traits, e.g., the 4S intermediate 2HBP-sulfinate (HBPS) behaves as an inhibitor of the Dsz monooxygenases, and once secreted from the cells it cannot be further taken up. That issue should be addressed for the rational design of more efficient biocatalysts for DBT bioconversions. In this sense, the construction of synthetic bacterial consortia to compartmentalize the 4S pathway into different cell factories for individual optimization was shown to enhance the conversion of DBT into 2HBP, overcome the inhibition of the Dsz enzymes by the 4S intermediates, and enable efficient production of unattainable high added value intermediates, e.g., HBPS, that are difficult to obtain using the current monocultures.
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Affiliation(s)
- Igor Martínez
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | | | - Daniel Rozas
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - José Luis García
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
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Paixão SM, Silva TP, Arez BF, Alves L. Advances in the Reduction of the Costs Inherent to Fossil Fuels' Biodesulfurization towards Its Potential Industrial Application. APPLYING NANOTECHNOLOGY TO THE DESULFURIZATION PROCESS IN PETROLEUM ENGINEERING 2016. [DOI: 10.4018/978-1-4666-9545-0.ch013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Biodesulfurization (BDS) process consists on the use of microorganisms for the removal of sulfur from fossil fuels. Through BDS it is possible to treat most of the organosulfur compounds recalcitrant to the conventional hydrodesulfurization (HDS), the petroleum industry's solution, at mild operating conditions, without the need for molecular hydrogen or metal catalysts. This technique results in lower emissions, smaller residue production and less energy consumption, which makes BDS an eco-friendly process that can complement HDS making it more efficient. BDS has been extensively studied and much is already known about the process. Clearly, BDS presents advantages as a complementary technique to HDS; however its commercial use has been delayed by several limitations both upstream and downstream the process. This study will comprehensively review and discuss key issues, like reduction of the BDS costs, advances and/or challenges for a competitive BDS towards its potential industrial application aiming ultra low sulfur fuels.
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Affiliation(s)
| | | | - Bruno F. Arez
- Laboratório Nacional de Energia e Geologia, Portugal
| | - Luís Alves
- Laboratório Nacional de Energia e Geologia, Portugal
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Abstract
The use of nanostructured materials in combination with desulfurizing microorganisms is a promising technique that would improve the desulfurization processes of gaseous fuels, oil, and some wastewater. Nanoparticles are highly versatile and tunable depending on the necessities of each particular contaminated media. The chapter shows the current technological options for the biodesulfurization of natural gas, oil and wastewater produced from the petroleum refining, where the application of nano-sized materials combined with desulfurizing microorganisms would improve the desulfurization capacities. In addition, advantages, disadvantages and opportunities of this hybrid technology are presented.
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Bhasarkar JB, Dikshit PK, Moholkar VS. Ultrasound assisted biodesulfurization of liquid fuel using free and immobilized cells of Rhodococcus rhodochrous MTCC 3552: A mechanistic investigation. BIORESOURCE TECHNOLOGY 2015; 187:369-378. [PMID: 25863901 DOI: 10.1016/j.biortech.2015.03.102] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/01/2015] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
This paper attempts to gain mechanistic insight into enhancement effect of sonication on biodesulfurization. The approach has been to fit Haldane kinetics model to dibenzothiophene (DBT) metabolism and analyze trends in model parameters concurrently with simulations of cavitation bubble dynamics. Mechanistic synergy between sonication and biodesulfurization is revealed to be of both physical and chemical nature. Generation of micro-turbulence in medium by sonication leads to fine emulsification and enhancement of DBT transport across organic/aqueous interphase. Microturbulence also enhances transport of substrate and product across cell wall that increases reaction velocity (Vmax). Michaelis constant (Km) and inhibition constant (KI), being intrinsic parameters, remain unaffected by sonication. Radicals produced by transient cavitation oxidize DBT to DBT-sulfoxide and DBT-sulfone (intermediates of metabolism), which contributes enhancement of biodesulfurization. However, high shear generated by ultrasound and cavitation has adverse effect on action of surfactant β-cyclodextrin for enhancement of interphase transport of DBT.
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Affiliation(s)
- Jaykumar B Bhasarkar
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Pritam Kumar Dikshit
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Vijayanand S Moholkar
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India.
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Guan LJ, Lee WC, Wang S, Ohshiro T, Izumi Y, Ohtsuka J, Tanokura M. Crystal structures of apo-DszC and FMN-bound DszC from Rhodococcus erythropolis D-1. FEBS J 2015; 282:3126-35. [PMID: 25627402 DOI: 10.1111/febs.13216] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 11/27/2022]
Abstract
UNLABELLED The release of SO2 from petroleum products derived from crude oil, which contains sulfur compounds such as dibenzothiophene (DBT), leads to air pollution. The '4S' metabolic pathway catalyzes the sequential conversion of DBT to 2-hydroxybiphenyl via three enzymes encoded by the dsz operon in several bacterial species. DszC (DBT monooxygenase), from Rhodococcus erythropolis D-1 is involved in the first two steps of the '4S' pathway. Here, we determined the first crystal structure of FMN-bound DszC, and found that two distinct conformations occur in the loop region (residues 131-142) adjacent to the active site. On the basis of the DszC-FMN structure and the previously reported apo structures of DszC homologs, the binding site for DBT and DBT sulfoxide is proposed. DATABASE The atomic coordinates and structure factors for apo-DszC (PDB code: 3X0X) and DszC-FMN (PDB code: 3X0Y) have been deposited in the Protein Data Bank (http://www.rcsb.org).
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Affiliation(s)
- Li-Jun Guan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Woo Cheol Lee
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shipeng Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takashi Ohshiro
- Department of Biotechnology, Tottori University, Koyama-Minami, Tottori, Japan
| | - Yoshikazu Izumi
- Department of Biotechnology, Tottori University, Koyama-Minami, Tottori, Japan
| | - Jun Ohtsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Akhtar N, Ghauri MA, Anwar MA, Heaphy S. Phylogenetic characterization and novelty of organic sulphur metabolizing genes of Rhodococcus spp. (Eu-32). Biotechnol Lett 2014; 37:837-47. [DOI: 10.1007/s10529-014-1736-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 11/19/2014] [Indexed: 11/29/2022]
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Khedkar S, Shanker R. Isolation and classification of a soil actinomycete capable of sulphur-specific biotransformation of dibenzothiophene, benzothiophene and thianthrene. J Appl Microbiol 2014; 118:62-74. [PMID: 25319398 DOI: 10.1111/jam.12665] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/12/2014] [Accepted: 10/13/2014] [Indexed: 01/08/2023]
Abstract
AIM To isolate actinomycete spp with the ability to desulphurize sulphur-containing heterocyclic compounds present in petroleum. METHODS AND RESULTS Enrichment cultures were set up to select and isolate sulphur heterocycle metabolizing soil micro-organisms. Screening of the microbial isolates for the desulphurization property led to isolation of R3. The isolate was characterized by PCR screening of 16S rRNA genes and classical taxonomic investigations. HPLC analysis of the desulphurization assays with R3 showed ~85% transformation of dibenzothiophene (270 μmol l(-1)), present as the sole sulphur source in basal salt medium, in 4 days. Production of the desulphurized dibenzothiophene metabolite, 2-hydroxybiphenyl, was confirmed by GC/MS analyses. GC/MS analyses also established the ability of R3 to transform benzothiophene to benzothiophene-1-oxide and benzothiophene-1, 1-dioxide, and thianthrene to thianthrene-5-oxide. PCR primers computed based on the desulphurization operon (dszABC) of Rhodococcus erythropolis IGTS8 yielded the predicted amplification products with R3 genomic DNA as template. Southern hybridization and restriction endonuclease digestion profiles indicated that R3 amplicons were homologous to dsz AB. CONCLUSIONS The enrichment method used in this study yielded an environmental isolate with the ability to transform multiple sulphur heterocycles. The isolate R3 has taxonomic proximity to the Oerskovia sp, order Actinomycetales. The isolate R3 selectively removes sulphur from dibenzothiophene yielding 2-hydroxybiphenyl and sulphate. R3 also transforms benzothiophene and thianthrene in a sulphur-targeted manner. The desulphurization genes in R3 bear similarity to those in R. erythropolis IGTS8. SIGNIFICANCE AND IMPACT OF THE STUDY The actinomycetes present in soil can remove sulphur from different sulphur heterocycle substrates and have potential as biodesulphurization catalysts.
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Affiliation(s)
- S Khedkar
- CSIR-National Environmental Engineering Research Institute, Nagpur, Maharashtra, India
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36
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Desulfurization of thianthrene by a Gordonia sp. IITR100. Biotechnol Lett 2014; 36:2209-14. [DOI: 10.1007/s10529-014-1606-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/26/2014] [Indexed: 11/25/2022]
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Liu S, Zhang C, Su T, Wei T, Zhu D, Wang K, Huang Y, Dong Y, Yin K, Xu S, Xu P, Gu L. Crystal structure of DszC from Rhodococcus sp. XP at 1.79 Å. Proteins 2014; 82:1708-20. [PMID: 24470304 DOI: 10.1002/prot.24525] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/02/2014] [Accepted: 01/16/2014] [Indexed: 11/07/2022]
Abstract
The dibenzothiophene (DBT) monooxygenase DszC, which is the key initiating enzyme in "4S" metabolic pathway, catalyzes sequential sulphoxidation reaction of DBT to DBT sulfoxide (DBTO), then DBT sulfone (DBTO2). Here, we report the crystal structure of DszC from Rhodococcus sp. XP at 1.79 Å. Intriguingly, two distinct conformations occur in the flexible lid loops adjacent to the active site (residue 280-295, between α9 and α10). They are named "open"' and "closed" state respectively, and might show the status of the free and ligand-bound DszC. The molecular docking results suggest that the reduced FMN reacts with an oxygen molecule at C4a position of the isoalloxazine ring, producing the C4a-(hydro)peroxyflavin intermediate which is stabilized by H391 and S163. H391 may contribute to the formation of the C4a-(hydro)peroxyflavin by acting as a proton donor to the proximal peroxy oxygen, and it might also be involved in the protonation process of the C4a-(hydro)xyflavin. Site-directed mutagenesis study shows that mutations in the residues involved either in catalysis or in flavin or substrate-binding result in a complete loss of enzyme activity, suggesting that the accurate positions of flavin and substrate are crucial for the enzyme activity.
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Affiliation(s)
- Shiheng Liu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
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Abro R, Abdeltawab AA, Al-Deyab SS, Yu G, Qazi AB, Gao S, Chen X. A review of extractive desulfurization of fuel oils using ionic liquids. RSC Adv 2014. [DOI: 10.1039/c4ra03478c] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Extractive desulfurization of fuel oils using ionic liquids as extractive reagents.
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Affiliation(s)
- Rashid Abro
- Beijing Key Laboratory of Membrane Science and Technology
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029, P. R. China
| | - Ahmed A. Abdeltawab
- Petrochemicals Research Chair
- College of Science
- King Saud University
- Riyadh 11451, Saudi Arabia
| | - Salem S. Al-Deyab
- Petrochemicals Research Chair
- College of Science
- King Saud University
- Riyadh 11451, Saudi Arabia
| | - Guangren Yu
- Beijing Key Laboratory of Membrane Science and Technology
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029, P. R. China
| | - Abdul Basit Qazi
- Beijing Key Laboratory of Membrane Science and Technology
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029, P. R. China
| | - Shurong Gao
- Beijing Key Laboratory of Membrane Science and Technology
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029, P. R. China
| | - Xiaochun Chen
- Beijing Key Laboratory of Membrane Science and Technology
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029, P. R. China
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Abin-Fuentes A, Mohamed MES, Wang DIC, Prather KLJ. Exploring the mechanism of biocatalyst inhibition in microbial desulfurization. Appl Environ Microbiol 2013; 79:7807-17. [PMID: 24096431 PMCID: PMC3837836 DOI: 10.1128/aem.02696-13] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/02/2013] [Indexed: 11/20/2022] Open
Abstract
Microbial desulfurization, or biodesulfurization (BDS), of fuels is a promising technology because it can desulfurize compounds that are recalcitrant to the current standard technology in the oil industry. One of the obstacles to the commercialization of BDS is the reduction in biocatalyst activity concomitant with the accumulation of the end product, 2-hydroxybiphenyl (HBP), during the process. BDS experiments were performed by incubating Rhodococcus erythropolis IGTS8 resting-cell suspensions with hexadecane at 0.50 (vol/vol) containing 10 mM dibenzothiophene. The resin Dowex Optipore SD-2 was added to the BDS experiments at resin concentrations of 0, 10, or 50 g resin/liter total volume. The HBP concentration within the cytoplasm was estimated to decrease from 1,100 to 260 μM with increasing resin concentration. Despite this finding, productivity did not increase with the resin concentration. This led us to focus on the susceptibility of the desulfurization enzymes toward HBP. Dose-response experiments were performed to identify major inhibitory interactions in the most common BDS pathway, the 4S pathway. HBP was responsible for three of the four major inhibitory interactions identified. The concentrations of HBP that led to a 50% reduction in the enzymes' activities (IC50s) for DszA, DszB, and DszC were measured to be 60 ± 5 μM, 110 ± 10 μM, and 50 ± 5 μM, respectively. The fact that the IC50s for HBP are all significantly lower than the cytoplasmic HBP concentration suggests that the inhibition of the desulfurization enzymes by HBP is responsible for the observed reduction in biocatalyst activity concomitant with HBP generation.
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Affiliation(s)
- Andres Abin-Fuentes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Daniel I. C. Wang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kristala L. J. Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Abin-Fuentes A, Leung JC, Mohamed MES, Wang DIC, Prather KLJ. Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system. Biotechnol Bioeng 2013; 111:876-84. [PMID: 24284557 DOI: 10.1002/bit.25148] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/31/2013] [Accepted: 11/04/2013] [Indexed: 11/05/2022]
Abstract
A mechanistic analysis of the various mass transport and kinetic steps in the microbial desulfurization of dibenzothiophene (DBT) by Rhodococcus erythropolis IGTS8 in a model biphasic (oil-water), small-scale system was performed. The biocatalyst was distributed into three populations, free cells in the aqueous phase, cell aggregates and oil-adhered cells, and the fraction of cells in each population was measured. The power input per volume (P/V) and the impeller tip speed (vtip ) were identified as key operating parameters in determining whether the system is mass transport controlled or kinetically controlled. Oil-water DBT mass transport was found to not be limiting under the conditions tested. Experimental results at both the 100 mL and 4 L (bioreactor) scales suggest that agitation leading to P/V greater than 10,000 W/ m(3) and/or vtip greater than 0.67 m/s is sufficient to overcome the major mass transport limitation in the system, which was the diffusion of DBT within the biocatalyst aggregates.
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Affiliation(s)
- Andres Abin-Fuentes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
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41
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Borzenkova NV, Veselova IA, Shekhovtsova TN. Biochemical methods of crude hydrocarbon desulfurization. ACTA ACUST UNITED AC 2013. [DOI: 10.1134/s2079086413040026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bhatia S, Sharma DK. Thermophilic desulfurization of dibenzothiophene and different petroleum oils by Klebsiella sp. 13T. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2012; 19:3491-3497. [PMID: 22467237 DOI: 10.1007/s11356-012-0884-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/18/2012] [Indexed: 05/31/2023]
Abstract
PURPOSE Biodesulfurization (BDS) has the potential to desulfurize dibenzothiophene (DBT) and its alkylated derivatives, the compounds that are otherwise refractory to hydrodesulfurization (HDS). Thermophilic microorganisms are more appropriate to be used for BDS applications following HDS. The aim of the present study was to isolate a thermophilic microorganism and to explore its commercial relevance for BDS process. METHODS The desulfurizing thermophilic strain was isolated and enriched from various soil and water samples using sulfur free medium (SFM) supplemented with DBT. Microbiological and genomic approach was used to characterize the strain. Desulfurization reactions were carried out using DBT and petroleum oils at 45°C followed by different analytical procedures. RESULTS We report the isolation of a thermophilic bacterium Klebsiella sp. 13T from contaminated soils collected from petroleum refinery. HPLC analysis revealed that Klebsiella sp. 13T could desulfurize DBT to 2-hydroxybiphenyl (2-HBP) at 45°C through 4S pathway. In addition, adapted cells of Klebsiella sp. 13T were found to remove 22-53% of sulfur from different petroleum oils with highest sulfur removal from light crude oil. CONCLUSION Klebsiella sp. 13T is a potential candidate for BDS because of its thermophilic nature and capability to desulfurize petroleum oils.
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Affiliation(s)
- Sumedha Bhatia
- Center for Energy Studies, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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43
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Chandra Srivastava V. An evaluation of desulfurization technologies for sulfur removal from liquid fuels. RSC Adv 2012. [DOI: 10.1039/c1ra00309g] [Citation(s) in RCA: 567] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Aggarwal S, Karimi IA, Kilbane II JJ, Lee DY. Roles of sulfite oxidoreductase and sulfite reductase in improving desulfurization by Rhodococcus erythropolis. MOLECULAR BIOSYSTEMS 2012; 8:2724-32. [DOI: 10.1039/c2mb25127b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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C-S targeted biodegradation of dibenzothiophene by Stenotrophomonas sp. NISOC-04. Appl Biochem Biotechnol 2011; 165:938-48. [PMID: 21750993 DOI: 10.1007/s12010-011-9310-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 06/19/2011] [Indexed: 10/18/2022]
Abstract
Crude oil-contaminated soil samples were gathered across Khuzestan oilfields (National Iranian South Oil Company, NISOC) consequently experienced a screening procedure for isolating C-S targeted dibenzothiophene-biodegrading microorganisms with previously optimized techniques. Among the isolates, a bacterial strain was selected due to its capability of biodegrading dibenzothiophene in a C-S targeted manner in aqueous phases and medium mostly consisting of separately biphasic water-gasoline. The 16S rDNA of the isolate was amplified using eubacterial-specific primers and then sequenced. Based on sequence data analysis, the microorganism, designated NISOC-04, clustered most closely with the members of the genus Stenotrophomonas. Gas chromatography indicated that Stenotrophomonas sp. NISOC-04 utilizes 82% of starting 0.8 mM dibenzothiophene within a 48-h-long exponential growth phase. Growth curve analysis revealed the inability of Stenotrophomonas sp. NISOC-04 to utilize dibenzothiophene (DBT) as the exclusive carbon or carbon/sulfur source. Gibbs' assay showed no 2-hydroxy biphenyl accumulation, but HPLC confirmed the presence of 2-hydroxy biphenyl as the final product of DBT desulfurization. Under sulfur starvation, Stenotrophomonas sp. NISOC-04 produced a huge biomass with untraceable sulfur and utilized atmospheric insignificant sulfur levels.
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Wang ZL, Wang D, Li Q, Li WL, Tang H, Xing JM. Enhanced biodesulfurization by expression of dibenzothiophene uptake genes in Rhodococcus erythropolis. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0656-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bahuguna A, Lily MK, Munjal A, Singh RN, Dangwal K. Desulfurization of dibenzothiophene (DBT) by a novel strain Lysinibacillus sphaericus DMT-7 isolated from diesel contaminated soil. J Environ Sci (China) 2011; 23:975-982. [PMID: 22066220 DOI: 10.1016/s1001-0742(10)60504-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A new bacterial strain DMT-7 capable of selectively desulfurizing dibenzothiophene (DBT) was isolated from diesel contaminated soil. The DMT-7 was characterized and identified as Lysinibacillus sphaericus DMT-7 (NCBI GenBank Accession No. GQ496620) using 16S rDNA gene sequence analysis. The desulfurized product of DBT, 2-hydroxybiphenyl (2HBP), was identified and confirmed by high performance liquid chromatography analysis and gas chromatography-mass spectroscopy analysis respectively. The desulfurization kinetics revealed that DMT-7 started desulfurization of DBT into 2HBP after the lag phase of 24 hr, exponentially increasing the accumulation of 2HBP up to 15 days leading to approximately 60% desulfurization of the DBT. However, further growth resulted into DBT degradation. The induced culture of DMT-7 showed shorter lag phase of 6 hr and early onset of stationary phase within 10 days for desulfurization as compared to that of non-induced culture clearly indicating the inducibility of the desulfurization pathway of DMT-7. In addition, Lysinibacillus sphaericus DMT-7 also possess the ability to utilize broad range of substrates as sole source of sulfur such as benzothiophene, 3,4-benzo DBT, 4,6-dimethyl DBT, and 4,6-dibutyl DBT. Therefore, Lysinibacillus sphaericus DMT-7 could serve as model system for efficient biodesulfurization of diesel and petrol.
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Affiliation(s)
- Ashutosh Bahuguna
- Department of Biotechnology, Modern Institute of Technology (MIT), Dhalwala, Rishikesh 249201, Uttarakhand, India.
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Shavandi M, Sadeghizadeh M, Khajeh K, Mohebali G, Zomorodipour A. Genomic structure and promoter analysis of the dsz operon for dibenzothiophene biodesulfurization from Gordonia alkanivorans RIPI90A. Appl Microbiol Biotechnol 2010; 87:1455-61. [PMID: 20414649 DOI: 10.1007/s00253-010-2605-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 04/03/2010] [Accepted: 04/04/2010] [Indexed: 10/19/2022]
Abstract
The bacterium Gordonia alkanivorans RIPI90A has been previously reported as dibenzothiophene-desulfurizing strain. The present study provides a complete investigation of the dsz operon including dsz promoter analysis from desulfurization competent strain belonging to the genus Gordonia. PCR was used to amplify the dszABC genes and adaptor ligation-based PCR-walking strategy used to isolate the dsz promoter. Unlike the dsz operon of Rhodococcus erythropolis, the operon of RIPI90A was located on chromosome. Despite the remarkably high homology between dsz genes of G. alkanivorans RIPI90A and R. erythropolis IGST8, promoter sequences of the strains were not very similar. The dsz promoter of G. alkanivorans RIPI90A shows only 52.5% homology to that of R. erythropolis IGTS8 and Gordonia nitida. Deletion analysis of the dsz promoter from RIPI90A using luciferase as a reporter gene revealed that the dsz promoter was located in regions from -156 to -50.
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Affiliation(s)
- Mahmoud Shavandi
- Department of Biotechnology, Biotechnology Research Center, Research Institute of Petroleum Industry, West Blvd. Azadi Sport Complex, Tehran, Iran.
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Site-directed mutagenesis enhances the activity of NADH-FMN oxidoreductase (DszD) activity of Rhodococcus erythropolis. Biotechnol Lett 2010; 32:921-7. [DOI: 10.1007/s10529-010-0254-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 03/09/2010] [Indexed: 11/25/2022]
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Ellis HR. The FMN-dependent two-component monooxygenase systems. Arch Biochem Biophys 2010; 497:1-12. [PMID: 20193654 DOI: 10.1016/j.abb.2010.02.007] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 02/13/2010] [Accepted: 02/16/2010] [Indexed: 11/19/2022]
Abstract
The FMN-dependent two-component monooxygenase systems catalyze a diverse range of reactions. These two-component systems are composed of an FMN reductase enzyme and a monooxygenase enzyme that catalyze the oxidation of various substrates. The role of the reductase is to supply reduced flavin to the monooxygenase enzyme, while the monooxygenase enzyme utilizes the reduced flavin to activate molecular oxygen. Unlike flavoproteins with a tightly or covalently bound prosthetic group, these enzymes catalyze the reductive and oxidative half-reaction on two separate enzymes. An interesting feature of these enzymes is their ability to transfer reduced flavin from the reductase to the monooxygenase enzyme. This review covers the reported mechanistic and structural properties of these enzyme systems, and evaluates the mechanism of flavin transfer.
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Affiliation(s)
- Holly R Ellis
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
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