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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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Hernik D, Gatti F, Brenna E, Szczepańska E, Olejniczak T, Boratyński F. Stereoselective synthesis of whisky lactone isomers catalyzed by bacteria in the genus Rhodococcus. Front Microbiol 2023; 14:1117835. [PMID: 36744099 PMCID: PMC9893411 DOI: 10.3389/fmicb.2023.1117835] [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: 12/06/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
Whisky lactone is a naturally occurring fragrance compound in oak wood and is widely used as a sensory additive in food products. However, safe and efficient methods for the production of its individual enantiomers for applications in the food industry are lacking. The aim of this study was to develop an efficient and highly stereoselective process for the synthesis of individual enantiomeric forms of whisky lactones. The proposed three-step method involves (1) column chromatography separation of a diastereoisomeric mixture of whisky lactone, (2) chemical reduction of cis-and trans-whisky lactones to corresponding syn-and anti-diols, and (3) microbial oxidation of racemic diols to individual enantiomers of whisky lactone. Among various bacteria in the genera Dietzia, Gordonia, Micrococcus, Rhodococcus, and Streptomyces, R. erythropolis DSM44534 and R. erythropolis PCM2150 effectively oxidized anti-and syn-3-methyl-octane-1,4-diols (1a-b) to corresponding enantiomerically pure cis-and trans-whisky lactones, indicating high alcohol dehydrogenase activity. Bio-oxidation catalyzed by whole cells of these strains yielded enantiomerically pure isomers of trans-(+)-(4S,5R) (2a), trans-(-)-(4R,5S) (2b), and cis-(+)-(4R,5R) (2d) whisky lactones. The optical density of bacterial cultures and the impact of the use of acetone powders as catalysts on the course of the reaction were also evaluated. Finally, the application of R. erythropolis DSM44534 in the form of an acetone powder generated the enantiomerically enriched cis-(-)-(4S,5S)-isomer (2c) from the corresponding syn-diol (1b). The newly developed method provides an improved approach for the synthesis of chiral whisky lactones.
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Affiliation(s)
- Dawid Hernik
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland,*Correspondence: Dawid Hernik, ✉
| | - Francesco Gatti
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Milano, Italy
| | - Elisabetta Brenna
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Milano, Italy
| | - Ewa Szczepańska
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Teresa Olejniczak
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Filip Boratyński
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland,Filip Boratyński, ✉
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Liu H, Liu S, Liu H, Liu M, Yin X, Lu P, Hong Q, Liu A, Wan R, Fang S. Revealing the driving synergistic degradation mechanism of Rhodococcus sp. B2 on the bioremediation of pretilachlor-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159086. [PMID: 36179826 DOI: 10.1016/j.scitotenv.2022.159086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
The pretilachlor has been widely used worldwide and has contaminated the environment for many years. The environmental fate of pretilachlor and its residues removal from the contaminated environment have attracted great concern. Reportedly, pretilachlor could partly be transformed to HECDEPA by Rhodococcus sp. B2. However, the effects of pretilachlor on soil bacterial communities and its complete metabolic pathway remain unknown. Herein, we investigated the mechanism of driving synergistic degradation of pretilachlor by strain B2 in the soil. The results revealed that pretilachlor showed a negative effect on bacterial communities and caused significant variations in the community structure. Strain B2 showed the ability to remediate the pretilachlor-contaminated soils and network analysis revealed that it may drive the enrichment of potential pretilachlor-degrading bacteria from the soil. The soil pretilachlor degradation may be facilitated by the members of the keystone families Comamonadaceae, Caulobacteraceae, Rhodospirillaceae, Chitinophagaceae, and Sphingomonadaceae. Meanwhile, Sphingomonas sp. M6, a member of the Sphingomonadaceae family, has been isolated from the strain B2 inoculation sample soil. The co-culture, comprising strain M6 and B2, could synergistic degrade pretilachlor within 30 h, which is the highest degradation rate. Strain M6 could completely degrade the HECDEPA via CDEPA and DEA. In the soil, a comparable pretilachlor degradation pathway may exist. This study suggested that strain B2 had the potential to drive the remediation of pretilachlor-contaminated soils.
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Affiliation(s)
- Hongming Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China.
| | - Shiyan Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Huijun Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Mengna Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Xiaye Yin
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Peng Lu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Qing Hong
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Aimin Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Rui Wan
- School of Ecology and Environment, Anhui Normal University, South of Jiuhua Road, Wuhu, Anhui 241002, China.
| | - Shangping Fang
- School of Anesthesiology, Wannan Medical College, Wuhu, Anhui, China
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El-malek FA, Farag A, Omar S, Khairy H. Polyhydroxyalkanoates (PHA) from Halomonas pacifica ASL10 and Halomonas salifodiane ASL11 isolated from Mariout salt lakes. Int J Biol Macromol 2020; 161:1318-1328. [DOI: 10.1016/j.ijbiomac.2020.07.258] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022]
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Busch H, Hagedoorn PL, Hanefeld U. Rhodococcus as A Versatile Biocatalyst in Organic Synthesis. Int J Mol Sci 2019; 20:E4787. [PMID: 31561555 PMCID: PMC6801914 DOI: 10.3390/ijms20194787] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
The application of purified enzymes as well as whole-cell biocatalysts in synthetic organic chemistry is becoming more and more popular, and both academia and industry are keen on finding and developing novel enzymes capable of performing otherwise impossible or challenging reactions. The diverse genus Rhodococcus offers a multitude of promising enzymes, which therefore makes it one of the key bacterial hosts in many areas of research. This review focused on the broad utilization potential of the genus Rhodococcus in organic chemistry, thereby particularly highlighting the specific enzyme classes exploited and the reactions they catalyze. Additionally, close attention was paid to the substrate scope that each enzyme class covers. Overall, a comprehensive overview of the applicability of the genus Rhodococcus is provided, which puts this versatile microorganism in the spotlight of further research.
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Affiliation(s)
- Hanna Busch
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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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: 4.4] [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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Arous F, Hamdi C, Kmiha S, Khammassi N, Ayari A, Neifar M, Mechichi T, Jaouani A. Treatment of olive mill wastewater through employing sequencing batch reactor: performance and microbial diversity assessment. 3 Biotech 2018; 8:481. [PMID: 30456015 DOI: 10.1007/s13205-018-1486-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/19/2018] [Indexed: 11/25/2022] Open
Abstract
This work describes the performance of a sequencing batch reactor (SBR) and the involvement of a novel reconstituted bacterial consortium in olive mill wastewater (OMW) treatment. The organic loading rate applied to the SBR was serially increased in terms of initial COD from 10 to 75 g L-1 to allow gradual acclimatization of activated sludge to high concentrations of toxic compounds in OMW. After the acclimatization period, up to 60% of the total COD content were effectively biodegraded from OMW at 75 g L-1 COD within 30 day hydraulic retention time. The diversity and community composition of cultivable bacteria participating in the aerobic process of treating OMW were further assessed. A total of 91 bacterial strains were isolated from the reactor and analyzed by amplification of the 16S-23S rRNA internal transcribed spacer (ITS) region and by 16S rRNA gene sequencing. The most abundant phylum was Firmicutes (57.1%) followed by Proteobacteria (35.2%) and Actinobacteria (7.7%). The use of the Biolog® Phenotype Microarray system to evaluate the ability of isolated strains to utilize OMW phenolic compounds is reported in this work for the first time. Interestingly, results showed that all species tested were able to utilize phenolics as sole carbon and energy sources. The removals of COD and phenolics from undiluted OMW by the reconstituted bacterial consortium were almost similar to those obtained by the acclimatized activated sludge, which suggest that cultivable bacteria play the major role in OMW biodegradation. Phytotoxicity assays using tomato seeds showed a significant improvement of seed germination values for treated OMW. Our overall results suggest that the novel developed bacterial consortium could be considered as a good prospect for phenolics-rich wastewaters bioremediation applications.
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Affiliation(s)
- Fatma Arous
- 1Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, University of Tunis El Manar, 9, Rue Zouhair Essafi, 1007 Tunis, Tunisia
| | - Chadlia Hamdi
- 1Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, University of Tunis El Manar, 9, Rue Zouhair Essafi, 1007 Tunis, Tunisia
| | - Souhir Kmiha
- 1Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, University of Tunis El Manar, 9, Rue Zouhair Essafi, 1007 Tunis, Tunisia
| | - Nadia Khammassi
- 1Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, University of Tunis El Manar, 9, Rue Zouhair Essafi, 1007 Tunis, Tunisia
| | - Amani Ayari
- 1Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, University of Tunis El Manar, 9, Rue Zouhair Essafi, 1007 Tunis, Tunisia
| | - Mohamed Neifar
- 2University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Tahar Mechichi
- 3Laboratoire de Biochimie et de Genie Enzymatique des Lipases, ENIS, Route de Soukra, BPW 1173-3038, Sfax, Tunisia
| | - Atef Jaouani
- 1Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, University of Tunis El Manar, 9, Rue Zouhair Essafi, 1007 Tunis, Tunisia
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Basu S, Rabara RC, Negi S, Shukla P. Engineering PGPMOs through Gene Editing and Systems Biology: A Solution for Phytoremediation? Trends Biotechnol 2018; 36:499-510. [DOI: 10.1016/j.tibtech.2018.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 01/17/2023]
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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: 42] [Impact Index Per Article: 6.0] [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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Dimitrova NH, Dermen IA, Todorova ND, Vasilev KG, Dimitrov SD, Mekenyan OG, Ikenaga Y, Aoyagi T, Zaitsu Y, Hamaguchi C. CATALOGIC 301C model - validation and improvement. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:511-524. [PMID: 28728491 DOI: 10.1080/1062936x.2017.1343255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
In Europe, REACH legislation encourages the use of alternative in silico methods such as (Q)SAR models. According to the recent progress of Chemical Substances Control Law (CSCL) in Japan, (Q)SAR predictions are also utilized as supporting evidence for the assessment of bioaccumulation potential of chemicals along with read across. Currently, the effective use of read across and QSARs is examined for other hazards, including biodegradability. This paper describes the results of external validation and improvement of CATALOGIC 301C model based on more than 1000 tested new chemical substances of the publication schedule under CSCL. CATALOGIC 301C model meets all REACH requirements to be used for biodegradability assessment. The model formalism built on scientific understanding for the microbial degradation of chemicals has a well-defined and transparent applicability domain. The model predictions are adequate for the evaluation of the ready degradability of chemicals.
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Affiliation(s)
- N H Dimitrova
- a Laboratory of Mathematical Chemistry , University "Prof. As. Zlatarov" , Bourgas , Bulgaria
| | - I A Dermen
- a Laboratory of Mathematical Chemistry , University "Prof. As. Zlatarov" , Bourgas , Bulgaria
| | - N D Todorova
- a Laboratory of Mathematical Chemistry , University "Prof. As. Zlatarov" , Bourgas , Bulgaria
| | - K G Vasilev
- a Laboratory of Mathematical Chemistry , University "Prof. As. Zlatarov" , Bourgas , Bulgaria
| | - S D Dimitrov
- a Laboratory of Mathematical Chemistry , University "Prof. As. Zlatarov" , Bourgas , Bulgaria
| | - O G Mekenyan
- a Laboratory of Mathematical Chemistry , University "Prof. As. Zlatarov" , Bourgas , Bulgaria
| | - Y Ikenaga
- b Chemical Management Center, National Institute of Technology and Evaluation (NITE) , Japan
| | - T Aoyagi
- b Chemical Management Center, National Institute of Technology and Evaluation (NITE) , Japan
| | - Y Zaitsu
- b Chemical Management Center, National Institute of Technology and Evaluation (NITE) , Japan
| | - C Hamaguchi
- b Chemical Management Center, National Institute of Technology and Evaluation (NITE) , Japan
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Pi Y, Chen B, Bao M, Fan F, Cai Q, Ze L, Zhang B. Microbial degradation of four crude oil by biosurfactant producing strain Rhodococcus sp. BIORESOURCE TECHNOLOGY 2017; 232:263-269. [PMID: 28236759 DOI: 10.1016/j.biortech.2017.02.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 06/06/2023]
Abstract
Rhodococcus erythropolis M-25, one of the representative biosurfactant producers, performed effectively during the biodegradation of four crude oil. The microbial degradation efficiency is positively relevant to the API of the crude oil. The chemical dispersant Corexit 9500A did not enhance the biodegradation of the petroleum hydrocarbons during the experimental period. 70.7% of the N-4 oil was degraded after 30days, while in the Corexit 9500A plus sample the biodegradation removal was 42.8%. The Corexit-derived compounds were metabolized by M-25 at the same time of the petroleum hydrocarbons biodegrading. Neither biodegradation nor chemical dispersion process has almost no effect on the biomarker (m/z=231). The saturated methyl-branched fatty acids increased from 37.3%, to 49.4%, when M-25 was exposed with the N-4 crude oil. Similarly, the saturated methyl-branched fatty acids in the membrane of N3-2P increased from 20.25% to 44.1%, when exposed it with the N-4 crude oil.
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Affiliation(s)
- Yongrui Pi
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, Shandong 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, China; Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B3X5, Canada
| | - Bing Chen
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B3X5, Canada
| | - Mutai Bao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, Shandong 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, China.
| | - Fuqiang Fan
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B3X5, Canada
| | - Qinhong Cai
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B3X5, Canada
| | - Lv Ze
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B3X5, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B3X5, Canada
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Genome and Proteome Analysis of Rhodococcus erythropolis MI2: Elucidation of the 4,4´-Dithiodibutyric Acid Catabolism. PLoS One 2016; 11:e0167539. [PMID: 27977722 PMCID: PMC5157978 DOI: 10.1371/journal.pone.0167539] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/15/2016] [Indexed: 01/02/2023] Open
Abstract
Rhodococcus erythropolis MI2 has the extraordinary ability to utilize the xenobiotic 4,4´-dithiodibutyric acid (DTDB). Cleavage of DTDB by the disulfide-reductase Nox, which is the only verified enzyme involved in DTDB-degradation, raised 4-mercaptobutyric acid (4MB). 4MB could act as building block of a novel polythioester with unknown properties. To completely unravel the catabolism of DTDB, the genome of R. erythropolis MI2 was sequenced, and subsequently the proteome was analyzed. The draft genome sequence consists of approximately 7.2 Mbp with an overall G+C content of 62.25% and 6,859 predicted protein-encoding genes. The genome of strain MI2 is composed of three replicons: one chromosome and two megaplasmids with sizes of 6.45, 0.4 and 0.35 Mbp, respectively. When cells of strain MI2 were cultivated with DTDB as sole carbon source and compared to cells grown with succinate, several interesting proteins with significantly higher expression levels were identified using 2D-PAGE and MALDI-TOF mass spectrometry. A putative luciferase-like monooxygenase-class F420-dependent oxidoreductase (RERY_05640), which is encoded by one of the 126 monooxygenase-encoding genes of the MI2-genome, showed a 3-fold increased expression level. This monooxygenase could oxidize the intermediate 4MB into 4-oxo-4-sulfanylbutyric acid. Next, a desulfurization step, which forms succinic acid and volatile hydrogen sulfide, is proposed. One gene coding for a putative desulfhydrase (RERY_06500) was identified in the genome of strain MI2. However, the gene product was not recognized in the proteome analyses. But, a significant expression level with a ratio of up to 7.3 was determined for a putative sulfide:quinone oxidoreductase (RERY_02710), which could also be involved in the abstraction of the sulfur group. As response to the toxicity of the intermediates, several stress response proteins were strongly expressed, including a superoxide dismutase (RERY_05600) and an osmotically induced protein (RERY_02670). Accordingly, novel insights in the catabolic pathway of DTDB were gained.
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Khairy H, Wübbeler JH, Steinbüchel A. The NADH:flavin oxidoreductase Nox from Rhodococcus erythropolis MI2 is the key enzyme of 4,4'-dithiodibutyric acid degradation. Lett Appl Microbiol 2016; 63:434-441. [PMID: 27564089 DOI: 10.1111/lam.12662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/14/2016] [Accepted: 08/20/2016] [Indexed: 11/30/2022]
Abstract
The reduction of the disulphide bond is the initial catabolic step of the microbial degradation of the organic disulphide 4,4'-dithiodibutyric acid (DTDB). Previously, an NADH:flavin oxidoreductase from Rhodococcus erythropolis MI2 designated as NoxMI2 , which belongs to the old yellow enzyme (OYE) family, was identified. In the present study, it was proven that NoxMI2 has the ability to cleave the sulphur-sulphur bond in DTDB. In silico analysis revealed high sequence similarities to proteins of the flavin mononucleotide (FMN) reductase family identified in many strains of R. erythropolis. Therefore, nox was heterologously expressed in the pET23a(+) expression system using Escherichia coli strain BL21(DE3) pLysS, which effectively produces soluble active NoxMI2 . NoxMI2 showed a maximum specific activity (Vmax ) of 3·36 μmol min-1 mg-1 corresponding to a kcat of 2·5 s-1 and an apparent substrate Km of 0·6 mmol l-1 , when different DTDB concentrations were applied. No metal cofactors were required. Moreover, NoxMI2 had very low activity with other sulphur-containing compounds like 3,3'-dithiodipropionic acid (8·0%), 3,3'-thiodipropionic acid (7·6%) and 5,5'-dithiobis(2-nitrobenzoic acid) (8·0%). The UV/VIS spectrum of NoxMI2 revealed the presence of the cofactor FMN. Based on results obtained, NoxMI2 adds a new physiological substrate and mode of action to OYE members. SIGNIFICANCE AND IMPACT OF THE STUDY It was unequivocally demonstrated in this study that an NADH:flavin oxidoreductase from Rhodococcus erythropolis MI2 (NoxMI2 ) is able to cleave the xenobiotic disulphide 4,4'-dithiodibutyric acid (DTDB) into two molecules of 4-mercaptobutyric acid (4MB) with concomitant consumption of NADH. NoxMI2 showed a high substrate specificity as well as high heat stability. This study provides the first detailed characterization of the initial cleavage of DTDB, which is considered as a promising polythioester precursor.
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Affiliation(s)
- H Khairy
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany.,Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - J H Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - A Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany.,Faculty of Environmental Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Kilbane JJ. Biodesulfurization: How to Make it Work? ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2016. [DOI: 10.1007/s13369-016-2269-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Kilbane JJ, Stark B. Biodesulfurization: a model system for microbial physiology research. World J Microbiol Biotechnol 2016; 32:137. [DOI: 10.1007/s11274-016-2084-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 05/11/2016] [Indexed: 10/21/2022]
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