1
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Ferreira P, Neves RPP, Miranda FP, Cunha AV, Havenith RWA, Ramos MJ, Fernandes PA. DszA Catalyzes C-S Bond Cleavage through N 5-Hydroperoxyl Formation. J Chem Inf Model 2024; 64:4218-4230. [PMID: 38684937 PMCID: PMC11134501 DOI: 10.1021/acs.jcim.4c00301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization via the four enzymes of the metabolic 4S pathway of the bacterium Rhodococcus erythropolis (DszA-D) is a possible solution. However, the 4S pathway needs to operate at least 500 times faster for industrial applicability, a goal currently pursued through enzyme engineering. In this work, we unveil the catalytic mechanism of the flavin monooxygenase DszA. Surprisingly, we found that this enzyme follows a recently proposed atypical mechanism that passes through the formation of an N5OOH intermediate at the re side of the cofactor, aided by a well-defined, predominantly hydrophobic O2 pocket. Besides clarifying the unusual chemical mechanism of the complex DszA enzyme, with obvious implications for understanding the puzzling chemistry of flavin-mediated catalysis, the result is crucial for the rational engineering of DszA, contributing to making biodesulfurization attractive for the oil refining industry.
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Affiliation(s)
- Pedro Ferreira
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Rui P. P. Neves
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Filipa P. Miranda
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Ana V. Cunha
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerp 2000, Belgium
| | - Remco W. A. Havenith
- Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
- Ghent
Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan
281 (S3), Ghent B-9000, Belgium
| | - Maria J. Ramos
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Pedro A. Fernandes
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
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2
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Parveen S, Akhtar N, E-Kobon T, Burchmore R, Hussain AI, Akhtar K. Biodesulfurization of organosulfur compounds by a trehalose biosurfactant producing Gordonia sp. isolated from crude oil contaminated soil. World J Microbiol Biotechnol 2024; 40:103. [PMID: 38372854 DOI: 10.1007/s11274-024-03899-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
Certain factors hinder the commercialization of biodesulfurization process, including low substrate-specificity of the currently reported desulfurizing bacteria and restricted mass transfer of organic-sulfur compounds in biphasic systems. These obstacles must be addressed to clean organic-sulfur rich petro-fuels that pose serious environmental and health challenges. In current study, a dibenzothiophene desulfurizing strain, Gordonia rubripertincta W3S5 (source: oil contaminated soil) was systematically evaluated for its potential to remove sulfur from individual compounds and mixture of organic-sulfur compounds. Metabolic and genetic analyses confirmed that strain W3S5 desulfurized dibenzothiophene to 2-hydroxybiphenyl, suggesting that it follows the sulfur specific 4 S pathway. Furthermore, this strain demonstrated the ability to produce trehalose biosurfactants (with an EI24 of 53%) in the presence of dibenzothiophene, as confirmed by TLC and FTIR analyses. Various genome annotation tools, such as ClassicRAST, BlastKOALA, BV-BRC, and NCBI-PGAP, predicted the presence of otsA, otsB, treY, treZ, treP, and Trehalose-monomycolate lipid synthesis genes in the genomic pool of strain W3S5, confirming the existence of the OtsAB, TreYZ, and TreP pathways. Overall, these results underscore the potential of strain W3S5 as a valuable candidate for enhancing desulfurization efficiency and addressing the mass transfer challenges essential for achieving a scaled-up scenario.
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Affiliation(s)
- Sana Parveen
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad, 38000, Pakistan
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad, 38000, Pakistan.
| | - Teerasak E-Kobon
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Rd, Lat Yao, Chatuchak, Bangkok, 10900, Thailand
| | - Richard Burchmore
- School of Infection & Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Abdullah Ijaz Hussain
- Central Hi-Tech Lab, Department of Chemistry, Government College University, Faisalabad, 38000, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad, 38000, Pakistan
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3
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Crystallization, X-ray diffraction analysis and structure of ICMP from Pseudomonas aeruginosa. Biochem Biophys Res Commun 2022; 616:129-133. [DOI: 10.1016/j.bbrc.2022.05.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/15/2022]
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4
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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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5
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Efficient biodesulfurization of diesel oil by Gordonia sp. SC-10 with highly hydrophobic cell surfaces. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Liew JJM, El Saudi IM, Nguyen SV, Wicht DK, Dowling DP. Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond cleavage, substrate scope, and an unexpected role for the tetramer. J Biol Chem 2021; 297:100823. [PMID: 34029591 PMCID: PMC8234197 DOI: 10.1016/j.jbc.2021.100823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 02/01/2023] Open
Abstract
Bacterial two-component flavin-dependent monooxygenases cleave the stable C-S bond of environmental and anthropogenic organosulfur compounds. The monooxygenase MsuD converts methanesulfonate (MS-) to sulfite, completing the sulfur assimilation process during sulfate starvation, but the mechanism of this conversion remains unclear. To explore the mechanism of C-S bond cleavage, we report a series of crystal structures of MsuD from Pseudomonas fluorescens in different liganded states. This report provides the first crystal structures of an alkanesulfonate monooxygenase with a bound flavin and alkanesulfonate, elucidating the roles of the active site lid, the protein C terminus, and an active site loop in flavin and/or alkanesulfonate binding. These structures position MS- closest to the flavin N5 position, consistent with an N5-(hydro)peroxyflavin mechanism rather than a classical C4a-(hydro)peroxyflavin mechanism. A fully enclosed active site is observed in the ternary complex, mediated by interchain interaction of the C terminus at the tetramer interface. These structures identify an unexpected function of the protein C terminus in this protein family in stabilizing tetramer formation and the alkanesulfonate-binding site. Spurred by interest from the crystal structures, we conducted biochemical assays and molecular docking that redefine MsuD as a small- to medium-chain alkanesulfonate monooxygenase. Functional mutations verify the sulfonate-binding site and reveal the critical importance of the protein C terminus for monooxygenase function. These findings reveal a deeper understanding of MsuD's functionality at the molecular level and consequently how it operates within its role as part of the sulfur assimilation pathway.
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Affiliation(s)
- Jeremy J M Liew
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Israa M El Saudi
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Son V Nguyen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Denyce K Wicht
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Daniel P Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA.
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7
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A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis. Nat Commun 2021; 12:2092. [PMID: 33828077 PMCID: PMC8027225 DOI: 10.1038/s41467-021-22395-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
Streptoseomycin (STM, 1) is a bacterial macrolactone that has a unique 5/14/10/6/6-pentacyclic ring with an ether bridge. We have previously identified the biosynthetic gene cluster for 1 and characterized StmD as [6 + 4]- and [4 + 2]-bispericyclase that catalyze a reaction leading to both 6/10/6- and 10/6/6-tricyclic adducts (6 and 7). The remaining steps, especially how to install and stabilize the required 10/6/6-tricyclic core for downstream modifications, remain unknown. In this work, we have identified three oxidoreductases that fix the required 10/6/6-tryciclic core. A pair of flavin-dependent oxidoreductases, StmO1 and StmO2, catalyze the direct hydroxylation at [6 + 4]-adduct (6). Subsequently, a spontaneous [3,3]-Cope rearrangement and an enol-ketone tautomerization result in the formation of 10/6/6-tricyclic intermediate 12b, which can be further converted to a stable 10/6/6-tricyclic alcohol 11 through a ketoreduction by StmK. Crystal structure of the heterodimeric complex NtfO1-NtfO2, homologues of StmO1-StmO2 with equivalent function, reveals protein-protein interactions. Our results demonstrate that the [6 + 4]-adduct instead of [4 + 2]-adduct is the bona fide biosynthetic intermediate.
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8
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Nassar HN, Abu Amr SS, El-Gendy NS. Biodesulfurization of refractory sulfur compounds in petro-diesel by a novel hydrocarbon tolerable strain Paenibacillus glucanolyticus HN4. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:8102-8116. [PMID: 33048293 DOI: 10.1007/s11356-020-11090-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
One of the main precursors of air pollution and acid rains is the presence of the recalcitrant thiophenic compounds, for example dibenzothiophene (DBT) and its derivatives in transportation fuels. In an attempt to achieve the worldwide regulations of ultra-low sulfur transportation fuels without affecting its hydrocarbon skeleton, a biphasic medium containing 100 mg/L DBT dissolved in n-hexadecane (1/4 oil/water v/v) used for enrichment and isolation of selective biodesulfurizing bacterium from an oil-polluted sediment sample collected from Egyptian Red Sea shoreline. The isolated bacterium is facultative anaerobe, motile, spore-former, and mesophile. It is genetically identified as Paenibacillus glucanolyticus strain HN4 (NCBI Gene Bank Accession No. MT645230). HN4 desulfurized DBT as a model of the recalcitrant thiophenic compounds without affecting its hydrocarbon skeleton via the 4S-pathway producing 2-hydroxybiphenyl (2-HBP) as a dead end product. HN4 substantiated to be a hydrocarbon tolerant, biosurfactants(s) producer, and endorsed unique enzymatic system capable of desulfurizing broad range of thiophenic compounds and expressed an efficient desulfurization activity against the recalcitrant alkylated DBTs. As far our knowledge, it is the first reported BDS study using P. glucanolyticus. Statistical optimization based on One-Factor-At-A-Time (OFAT) technique and response surface methodology (RSM) applied for elucidation of mathematical model correlations describing and optimizing the effect of different physicochemical parameters on batch biphasic BDS process. That illustrated an approximate increase in BDS efficiency by 1.34 fold and recorded 94% sulfur removal in biphasic batch process at optimum operation conditions of 120 h, 0.14 wt% S-content model oil (DBT dissolved in n-hexadecane), 33.5 °C, pH7 and 1/1 oil/water phase ratio, and 147 rpm. Resting cells of HN4 in a biphasic reactor (1/1 v/v) decreased the sulfur content of a refractory thiophenic model oil (thiophene, benzothiophene, DBT, and alkylated DBT dissolved in n-hexadecane) from 0.14 to 0.027 wt%, and petro-diesel from 0.2 to 0.04 wt%, within 120 h, keeping the calorific value of the treated fuel intact. Consequently, that novel strain could be recommended as a promising candidate for BDS as complementary to hydrodesulfurization process in oil refinery.
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Affiliation(s)
- Hussein N Nassar
- Petroleum Biotechnology Lab., Department of Process Design and Development, Egyptian Petroleum Research Institute (EPRI), Nasr City, Cairo, 11727, Egypt
- Department of Microbiology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October City, Giza, 12566, Egypt
- Nanobiotechnology Program, Faculty of Nanotechnology for Postgraduate Studies, Cairo University, Sheikh Zayed Branch Campus, Sheikh Zayed City, Giza, 12588, Egypt
| | - Salem S Abu Amr
- Faculty of Engineering, Karabuk University, Demir Campus, 78050 Karabuk, Turkey
| | - Nour Sh El-Gendy
- Petroleum Biotechnology Lab., Department of Process Design and Development, Egyptian Petroleum Research Institute (EPRI), Nasr City, Cairo, 11727, Egypt.
- Nanobiotechnology Program, Faculty of Nanotechnology for Postgraduate Studies, Cairo University, Sheikh Zayed Branch Campus, Sheikh Zayed City, Giza, 12588, Egypt.
- Center of Excellence, October University for Modern Sciences and Arts (MSA), 6th of October City, Giza, 12566, Egypt.
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9
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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: 2.5] [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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10
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Dejaloud A, Habibi A, Vahabzadeh F. DBT desulfurization by Rhodococcus erythropolis PTCC 1767 in aqueous and biphasic systems. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01191-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Li L, Ye L, Lin Y, Zhang W, Liao X, Liang S. Enhancing the substrate tolerance of DszC by a combination of alanine scanning and site-directed saturation mutagenesis. J Ind Microbiol Biotechnol 2020; 47:395-402. [PMID: 32303871 DOI: 10.1007/s10295-020-02274-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/09/2020] [Indexed: 01/30/2023]
Abstract
The biodesulfurization 4S pathway can specifically desulfurize an aromatic S heterocyclic compound (which is difficult to desulfurize by hydrodesulfurization) and maintain the integrity of its combustion value. The four Dsz enzymes in the pathway convert the model compound dibenzothiophene (DBT) into the sulfur-free compound 2-hydroxybiphenyl (HBP). DszC is the first enzyme in the 4S pathway and is subject to feedback inhibition and substrate inhibition. This study is the first attempt to further modify the DszC mutant AKWC to improve its tolerance to DBT. Alanine scanning was performed on the dimeric surface of the DszC mutant AKWC, and the HBP yield of the BAD (AKWCP413A) strain was increased compared to the BAD (AKWC) strain. Site-directed saturation mutagenesis was performed on the 413th amino acid of AKWC, and the substrate inhibition parameter KI value of the mutant AKWCPI was 5.6 times higher than that of AKWC. When the DBT concentration was 0.25 mM, the HBP production of the recombinant strain overexpressing AKWCPI was increased by approximately 1.4-fold compared to the BL21(DE3)/BADC*+C* strain. The protein engineering of DszC further improved the substrate tolerance after overcoming the feedback inhibition, which provided a reference for the analysis of the inhibition mechanism of DszC substrate. Overexpression of DszC-beneficial mutants also greatly improved the efficiency of desulfurization.
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Affiliation(s)
- Lu Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, 510006, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Wei Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xihao Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
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12
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Li L, Liao Y, Luo Y, Zhang G, Liao X, Zhang W, Zheng S, Han S, Lin Y, Liang S. Improved Efficiency of the Desulfurization of Oil Sulfur Compounds in Escherichia coli Using a Combination of Desensitization Engineering and DszC Overexpression. ACS Synth Biol 2019; 8:1441-1451. [PMID: 31132321 DOI: 10.1021/acssynbio.9b00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 4S pathway of biodesulfurization, which can specifically desulfurize aromatic S-heterocyclic compounds without destroying their combustion value, is a low-cost and environmentally friendly technology that is complementary to hydrodesulfurization. The four Dsz enzymes convert the model compound dibenzothiophene (DBT) into the sulfur-free compound 2-hydroxybiphenyl (HBP). Of these four enzymes, DszC, the first enzyme in the 4S pathway, is the most severely affected by the feedback inhibition caused by HBP. This study is the first attempt to directly modify DszC to decrease its inhibition by HBP, with the results showing that the modified protein is insensitive to HBP. On the basis of the principle that the final HBP product could show a blue color with Gibbs reagent, a high-throughput screening method for its rapid detection was established. The screening method and the combinatorial mutagenesis generated the mutant AKWC (A101K/W327C) of DszC. After the IC50 was calculated, the feedback inhibition of the AKWC mutant was observed to have been substantially reduced. Interestingly, the substrate inhibition of DszC had also been reduced as a result of directed evolution. Finally, the recombinant BL21(DE3)/BADC*+C* (C* represents AKWC) strain exhibited a specific conversion rate of 214.84 μmolHBP/gDCW/h, which was 13.8-fold greater than that of the wild-type strain. Desensitization engineering and the overexpression of the desensitized DszC protein resulted in the elimination of the feedback inhibition bottleneck in the 4S pathway, which is practical and effective progress toward the production of sulfur-free fuel oil. The results of this study demonstrate the utility of desensitization of feedback inhibition regulation in metabolic pathways by protein engineering.
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Affiliation(s)
- Lu Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yibo Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yifan Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Guangming Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xihao Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wei Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Thermophilic biodesulfurization and its application in oil desulfurization. Appl Microbiol Biotechnol 2018; 102:9089-9103. [DOI: 10.1007/s00253-018-9342-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/19/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022]
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