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Ham S, Cho DH, Oh SJ, Hwang JH, Kim HJ, Shin N, Ahn J, Choi KY, Bhatia SK, Yang YH. Enhanced production of bio-indigo in engineered Escherichia coli, reinforced by cyclopropane-fatty acid-acyl-phospholipid synthase from psychrophilic Pseudomonas sp. B14-6. J Biotechnol 2023; 366:1-9. [PMID: 36849085 DOI: 10.1016/j.jbiotec.2023.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/29/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Indigo dye is an organic compound with a distinctive blue color. Most of the indigo currently used in industry is produced via chemical synthesis, which generates a large amount of wastewater. Therefore, several studies have recently been conducted to find ways to produce indigo eco-friendly using microorganisms. Here, we produced indigo using recombinant Escherichia coli with both an indigo-producing plasmid and a cyclopropane fatty acid (CFA)-regulating plasmid. The CFA-regulating plasmid contains the cfa gene, and its expression increases the CFA composition of the phospholipid fatty acids of the cell membrane. Overexpression of cfa showed cytotoxicity resistance of indole, an intermediate product formed during the indigo production process. This had a positive effect on indigo production and cfa originated from Pseudomonas sp. B 14-6 was used. Optimal conditions for indigo production were determined by adjusting the expression strain, culture temperature, shaking speed, and isopropyl β-D-1-thiogalactopyranoside concentration. Treatment with Tween 80 at a particular concentration to increase the permeability of the cell membrane had a positive effect on indigo production. The strain with the CFA plasmid produced 4.1 mM of indigo after 24 h of culture and produced 1.5-fold higher indigo than the control strain without the CFA plasmid that produced 2.7 mM.
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Affiliation(s)
- Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Do-Hyun Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Suk Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Nara Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, Korea Research Institute Bioscience Biotechnology (KRIBB), the Republic of Korea
| | - Kwon-Young Choi
- Department of Environmental and Safety Engineering, College of Engineering, Ajou University, the Republic of Korea; Department of Energy Systems Research, Ajou University, the Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea.
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea.
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Production of Indigo by Recombinant Escherichia coli with Expression of Monooxygenase, Tryptophanase, and Molecular Chaperone. Foods 2022; 11:foods11142117. [PMID: 35885360 PMCID: PMC9320885 DOI: 10.3390/foods11142117] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022] Open
Abstract
Indigo is an important pigment widely used in industries of food, cosmetics, and textile. In this work, the styrene monooxygenase StyAB from Pseudomonas putida was co-expressed with the tryptophanase TnaA and the chaperone groES-groEL in Escherichia coli for indigo production. Over-expression of the gene styAB endowed the recombinant E. coli AB with the capacity of indigo biosynthesis from indole and tryptophan. Tryptophan fermentation in E. coli AB generated about five times more indigo than that from indole, and the maximum 530 mg/L of indigo was obtained from 1.2 mg/mL of tryptophan. The gene TnaA was then co-expressed with styAB, and the tryptophanase activity significantly increased in the recombinant E. coli ABT. However, TnaA expression led to a decrease in the activity of StyAB and indigo yield in E. coli ABT. Furthermore, the plasmid pGro7 harboring groES-groEL was introduced into E. coli AB, which obviously promoted the activity of StyAB and accelerated indigo biosynthesis in the recombinant E. coli ABP. In addition, the maximum yield of indigo was further increased to 550 mg/L from 1.2 mg/mL of tryptophan in E. coli ABP. The genetic manipulation strategy proposed in this work could provide new insights into construction of indigo biosynthesis cell factory for industrial production.
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Yang J, Ma F, Dai C, Wu W, Fan S, Lian S, Qu Y. Indole metabolism by phenol-stimulated activated sludges: Performance, microbial communities and network analysis. ENVIRONMENTAL RESEARCH 2022; 207:112660. [PMID: 34995547 DOI: 10.1016/j.envres.2021.112660] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/03/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Indole and phenol often coexist in the coking wastewater, while the effects of phenol on microbial communities of indole metabolism were less explored. In this study, the microbial interactions within activated sludge microbial communities stimulated by indole (group A) or by indole and phenol (group B) were systematically investigated in sequencing batch reactors (SBRs). The results showed that the removal of indole was increased by adding phenol. By using high-throughput sequencing technology, it was found that α-diversity was reduced in both groups. According to the relative abundance analysis, the indole-degrading genus Comamonas was the core genus in both groups (33.94% and 61.40%). But another indole-degrading genus Pseudomonas was only enriched in group A with 12.22% relative abundance. Meanwhile, common aromatic degrading genus Dyella and Thermomonas were enriched only in group B. It was found that the relative abundance of cytochrome P450 and styrene degradation enzymes were increased in group B by PICRUSt analysis. Based on the phylogenetic molecular ecological networks (pMENs), module hub OTU_1149 (Burkholderia) was only detected in group B, and the positive interactions between the key functional genus Burkholderia and other bacteria were increased. This study provides new insights into our understanding of indole metabolism communities stimulated by phenol, which would provide useful information for practical coking wastewater treatment.
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Affiliation(s)
- Jing Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Chunxiao Dai
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Weize Wu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Shuling Fan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Shengyang Lian
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
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Ramchandran R, Ramesh S, A A, Thakur R, Chakrabarti A, Roy U. Improved Production of Two Anti- Candida Lipopeptide Homologues Co- Produced by the Wild-Type Bacillus subtilis RLID 12.1 under Optimized Conditions. Curr Pharm Biotechnol 2019; 21:438-450. [PMID: 31804165 DOI: 10.2174/1389201020666191205115008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 10/21/2019] [Accepted: 11/06/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Antifungal cyclic lipopeptides, bioactive metabolites produced by many species of the genus Bacillus, are promising alternatives to synthetic fungicides and antibiotics for the biocontrol of human pathogenic fungi. In a previous study, the co- production of five antifungal lipopeptides homologues (designated as AF1, AF2, AF3, AF4 and AF5) by the producer strain Bacillus subtilis RLID 12.1 using unoptimized medium was reported; though the two homologues AF3 and AF5 differed by 14 Da and in fatty acid chain length were found effective in antifungal action, the production/ yield rate of these two lipopeptides determined by High-Performance Liquid Chromatography was less in the unoptimized media. METHODS In this study, the production/yield enhancement of the two compounds AF3 and AF5 was specifically targeted. Following the statistical optimization (Plackett-Burman and Box-Behnken designs) of media formulation, temperature and growth conditions, the production of AF3 and AF5 was improved by about 25.8- and 7.4-folds, respectively under static conditions. RESULTS To boost the production of these two homologous lipopeptides in the optimized media, heat-inactivated Candida albicans cells were used as a supplement resulting in 34- and 14-fold increase of AF3 and AF5, respectively. Four clinical Candida auris isolates had AF3 and AF5 MICs (100 % inhibition) ranging between 4 and 16 μg/ml indicating the lipopeptide's clinical potential. To determine the in vitro pharmacodynamic potential of AF3 and AF5, time-kill assays were conducted which showed that AF3 (at 4X and 8X concentrations) at 48h exhibited mean log reductions of 2.31 and 3.14 CFU/ml of C. albicans SC 5314, respectively whereas AF5 at 8X concentration showed a mean log reduction of 2.14 CFU/ml. CONCLUSION With the increasing threat of multidrug-resistant yeasts and fungi, these antifungal lipopeptides produced by optimized method promise to aid in the development of novel antifungal that targets disease-causing fungi with improved efficacy.
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Affiliation(s)
- Ramya Ramchandran
- Department of Biological Sciences, BITS Pilani K.K Birla Goa Campus, Goa 403726, India
| | - Swetha Ramesh
- Department of Biological Sciences, BITS Pilani K.K Birla Goa Campus, Goa 403726, India
| | - Anviksha A
- Department of Biological Sciences, BITS Pilani K.K Birla Goa Campus, Goa 403726, India
| | - RamLal Thakur
- Department of Microbiology, Sardar Bhagwan Singh Post Graduate Institute of Biomedical Science & Research, Balawala, Dehradun, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Utpal Roy
- Department of Biological Sciences, BITS Pilani K.K Birla Goa Campus, Goa 403726, India
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Dai C, Ma Q, Li Y, Zhou D, Yang B, Qu Y. Application of an efficient indole oxygenase system from Cupriavidus sp. SHE for indigo production. Bioprocess Biosyst Eng 2019; 42:1963-1971. [PMID: 31482396 DOI: 10.1007/s00449-019-02189-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 08/03/2019] [Indexed: 10/26/2022]
Abstract
Indigo, one of the most widely used dyes, is mainly produced by chemical processes, which generate amounts of pollutants and need high energy consumption. Microbial production of indigo from indole has attracted much attention; however, the indole oxygenase has never been explored and applied for indigo production. In the present study, the indole oxygenase indAB genes were successfully cloned from Cupriavidus sp. SHE and heterologously expressed in Escherichia coli BL21(DE3) (designated as IND_AB). Strain IND_AB produced primarily indigo in tryptophan medium by high-performance liquid chromatography-mass spectroscopy (HPLC-MS) analysis. The preferable conditions for indigo production were pH 6.5 (normal pH), 30 °C, 150 rpm, strain inoculation concentration OD600 0.08, and induction with 1 mM IPTG at the time of inoculation. The optimal culture medium compositions were further determined as tryptophan 1.0 g/L, NaCl 3.55 g/L, and yeast extract 5.12 g/L based on single-factor experiment and response surface methodology. The highest indigo yield was 307 mg/L, which was 4.39-fold higher than the original value. This is the first study investigating indigo production using the indole oxygenase system and the results highlighted its potential in bio-indigo industrial application.
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Affiliation(s)
- Chunxiao Dai
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Duandi Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Bingyu Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
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Kamelamela N, Zalesne M, Morimoto J, Robbat A, Wolfe BE. Indigo- and indirubin-producing strains of Proteus and Psychrobacter are associated with purple rind defect in a surface-ripened cheese. Food Microbiol 2018; 76:543-552. [PMID: 30166186 DOI: 10.1016/j.fm.2018.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 06/17/2018] [Accepted: 07/19/2018] [Indexed: 01/28/2023]
Abstract
The rinds of surface-ripened cheeses have expected aesthetic properties, including distinct colors, that contribute to overall quality and consumer acceptance. Atypical rind pigments are frequently reported in small-scale cheese production, but the causes of these color defects are largely unknown. We provide a potential microbial explanation for a striking purple rind defect in a surface-ripened cheese. A cheese producer in the United States reported to us several batches of a raw-milk washed-rind cheese with a distinctly purple rind. We isolated a Proteus species from samples with purple rind defect, but not from samples with typical rind pigments, suggesting that this strain of Proteus could be causing the defect. When provided tryptophan, a precursor in the indigo and indirubin biosynthesis pathway, the isolated strain of Proteus secreted purple-red pigments. A Psychrobacter species isolated from both purple and normal rinds also secreted purple-red pigments. Using thin-layer chromatography and liquid chromatography-mass spectrometry, we confirmed that these bacteria produced indigo and indirubin from tryptophan just as closely related bacteria make these compounds in purple urine bag syndrome in medical settings. Experimental cheese communities with or without Proteus and Psychrobacter confirmed that these Proteobacteria cause purple pigmentation of cheese rinds. Reports of purple rinds in two other cheeses from Europe and the observation of pigment production by Proteus and Psychrobacter strains isolated from other cheese rinds suggest that purple rind defect has the potential to be widespread in surface-ripened cheeses.
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Affiliation(s)
- Noelani Kamelamela
- Department of Biology, Tufts University, 200 Boston Ave., Medford, MA, 02155, USA
| | - Michael Zalesne
- Department of Biology, Tufts University, 200 Boston Ave., Medford, MA, 02155, USA
| | - Joshua Morimoto
- Tufts University Sensory and Science Center, Tufts University, 200 Boston Ave., Medford, MA 02155, USA; Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Albert Robbat
- Tufts University Sensory and Science Center, Tufts University, 200 Boston Ave., Medford, MA 02155, USA; Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, 200 Boston Ave., Medford, MA, 02155, USA; Tufts University Sensory and Science Center, Tufts University, 200 Boston Ave., Medford, MA 02155, USA.
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7
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Cheng L, Yin S, Chen M, Sun B, Hao S, Wang C. Enhancing Indigo Production by Over-Expression of the Styrene Monooxygenase in Pseudomonas putida. Curr Microbiol 2016; 73:248-54. [PMID: 27154464 DOI: 10.1007/s00284-016-1055-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/23/2016] [Indexed: 10/21/2022]
Abstract
As an important traditional blue dye, indigo has been used in food and textile industry for centuries, which can be produced via the styrene oxygenation pathway in Pseudomonas putida. Hence, the styrene monooxygenase gene styAB and oxide isomerase gene styC are over-expressed in P. putida to investigate their roles in indigo biosynthesis. RT-qPCR analysis indicated that transcriptions of styA and styB were increased by 2500- and 750-folds in the styAB over-expressed strain B4-01, compared with the wild-type strain B4, consequently significantly enhancing the indole monooxygenase activity. Transcription of styC was also increased by 100-folds in the styC over-expressed strain B4-02. Besides, styAB over-expression slightly up-regulated the transcription of styC in B4-01, while styC over-expression hardly exerted an effect on the transcriptional levels of styA and styB and indole monooxygenase activity in B4-02. Furthermore, shaking flask experiments showed that indigo production in B4-01 reached 52.13 mg L(-1) after 24 h, which was sevenfold higher than that in B4. But no obvious increase in indigo yield was observed in B4-02. Over-expression of styAB significantly enhanced the indigo production, revealing that the monooxygenase STYAB rather than oxide isomerase STYC probably acted as the key rate-limiting enzyme in the indigo biosynthesis pathway in P. putida. This work provided a new strategy for enhancing indigo production in Pseudomonas.
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Affiliation(s)
- Lei Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China.,School of Food and Chemical Engineering, Beijing Technology and Business University, 11 & 33 Fu Cheng Road, Hai Dian District, Beijing, 100048, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No. 11, Fu Cheng Road, Hai Dian District, Beijing, 100048, China
| | - Sheng Yin
- School of Food and Chemical Engineering, Beijing Technology and Business University, 11 & 33 Fu Cheng Road, Hai Dian District, Beijing, 100048, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No. 11, Fu Cheng Road, Hai Dian District, Beijing, 100048, China
| | - Min Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China
| | - Baoguo Sun
- School of Food and Chemical Engineering, Beijing Technology and Business University, 11 & 33 Fu Cheng Road, Hai Dian District, Beijing, 100048, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No. 11, Fu Cheng Road, Hai Dian District, Beijing, 100048, China
| | - Shuai Hao
- School of Food and Chemical Engineering, Beijing Technology and Business University, 11 & 33 Fu Cheng Road, Hai Dian District, Beijing, 100048, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No. 11, Fu Cheng Road, Hai Dian District, Beijing, 100048, China
| | - Chengtao Wang
- School of Food and Chemical Engineering, Beijing Technology and Business University, 11 & 33 Fu Cheng Road, Hai Dian District, Beijing, 100048, China. .,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No. 11, Fu Cheng Road, Hai Dian District, Beijing, 100048, China.
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Ma Q, Qu Y, Zhang X, Liu Z, Li H, Zhang Z, Wang J, Shen W, Zhou J. Systematic investigation and microbial community profile of indole degradation processes in two aerobic activated sludge systems. Sci Rep 2015; 5:17674. [PMID: 26657581 PMCID: PMC4675989 DOI: 10.1038/srep17674] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/03/2015] [Indexed: 01/26/2023] Open
Abstract
Indole is widely spread in various environmental matrices. Indole degradation by bacteria has been reported previously, whereas its degradation processes driven by aerobic microbial community were as-yet unexplored. Herein, eight sequencing batch bioreactors fed with municipal and coking activated sludges were constructed for aerobic treatment of indole. The whole operation processes contained three stages, i.e. stage I, glucose and indole as carbon sources; stage II, indole as carbon source; and stage III, indole as carbon and nitrogen source. Indole could be completely removed in both systems. Illumina sequencing revealed that alpha diversity was reduced after indole treatment and microbial communities were significantly distinct among the three stages. At genus level, Azorcus and Thauera were dominant species in stage I in both systems, while Alcaligenes, Comamonas and Pseudomonas were the core genera in stage II and III in municipal sludge system, Alcaligenes and Burkholderia in coking sludge system. In addition, four strains belonged to genera Comamonas, Burkholderia and Xenophilus were isolated using indole as sole carbon source. Burkholderia sp. IDO3 could remove 100 mg/L indole completely within 14 h, the highest degradation rate to date. These findings provide novel information and enrich our understanding of indole aerobic degradation processes.
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Affiliation(s)
- Qiao Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Ziyan Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Huijie Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Zhaojing Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Jingwei Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Wenli Shen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
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Lin GH, Chen HP, Shu HY. Detoxification of Indole by an Indole-Induced Flavoprotein Oxygenase from Acinetobacter baumannii. PLoS One 2015; 10:e0138798. [PMID: 26390211 PMCID: PMC4577076 DOI: 10.1371/journal.pone.0138798] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 09/03/2015] [Indexed: 11/17/2022] Open
Abstract
Indole, a derivative of the amino acid tryptophan, is a toxic signaling molecule, which can inhibit bacterial growth. To overcome indole-induced toxicity, many bacteria have developed enzymatic defense systems to convert indole to non-toxic, water-insoluble indigo. We previously demonstrated that, like other aromatic compound-degrading bacteria, Acinetobacter baumannii can also convert indole to indigo. However, no work has been published investigating this mechanism. Here, we have shown that the growth of wild-type A. baumannii is severely inhibited in the presence of 3.5 mM indole. However, at lower concentrations, growth is stable, implying that the bacteria may be utilizing a survival mechanism to oxidize indole. To this end, we have identified a flavoprotein oxygenase encoded by the iifC gene of A. baumannii. Further, our results suggest that expressing this recombinant oxygenase protein in Escherichia coli can drive indole oxidation to indigo in vitro. Genome analysis shows that the iif operon is exclusively present in the genomes of A. baumannii and Pseudomonas syringae pv. actinidiae. Quantitative PCR and Western blot analysis also indicate that the iif operon is activated by indole through the AraC-like transcriptional regulator IifR. Taken together, these data suggest that this species of bacteria utilizes a novel indole-detoxification mechanism that is modulated by IifC, a protein that appears to be, at least to some extent, regulated by IifR.
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Affiliation(s)
- Guang-Huey Lin
- Microbial Genetics Laboratory, Department of Microbiology, Tzu-Chi University, Hualien, Taiwan
| | - Hao-Ping Chen
- Department of Biochemistry, School of Medicine, Tzu-Chi University, Hualien, Taiwan
| | - Hung-Yu Shu
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
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10
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Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems. PLoS One 2015; 10:e0138455. [PMID: 26372223 PMCID: PMC4570806 DOI: 10.1371/journal.pone.0138455] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/31/2015] [Indexed: 12/02/2022] Open
Abstract
Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia colinagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. colinagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. colinagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0–30 days) (P < 0.001) but not in later stages (30–132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities.
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Qu Y, Shen E, Ma Q, Zhang Z, Liu Z, Shen W, Wang J, Li D, Li H, Zhou J. Biodegradation of indole by a newly isolated Cupriavidus sp. SHE. J Environ Sci (China) 2015; 34:126-32. [PMID: 26257355 DOI: 10.1016/j.jes.2015.01.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/23/2014] [Accepted: 01/05/2015] [Indexed: 05/18/2023]
Abstract
Indole, a typical nitrogen heterocyclic aromatic pollutant, is extensively spread in industrial wastewater. Microbial degradation has been proven to be a feasible approach to remove indole, whereas the microbial resources are fairly limited. A bacterial strain designated as SHE was isolated and found to be an efficient indole degrader. It was identified as Cupriavidus sp. according to 16S rRNA gene analysis. Strain SHE could utilize indole as the sole carbon source and almost completely degrade 100mg/L of indole within 24hr. It still harbored relatively high indole degradation capacity within pH4-9 and temperature 25°C-35°C. Experiments also showed that some heavy metals such as Mn(2+), Pb(2+) and Co(2+) did not pose severe inhibition on indole degradation. Based on high performance liquid chromatography-mass spectrum analysis, isatin was identified as a minor intermediate during the process of indole biodegradation. A major yellow product with m/z 265.0605 (C15H8N2O3) was generated and accumulated, suggesting a novel indole conversion pathway existed. Genome analysis of strain SHE indicated that there existed a rich set of oxidoreductases, which might be the key reason for the efficient degradation of indole. The robust degradation ability of strain SHE makes it a promising candidate for the treatment of indole containing wastewater.
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Affiliation(s)
- Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - E Shen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qiao Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhaojing Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ziyan Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Wenli Shen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwei Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Duanxing Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Huijie Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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12
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Genome Sequence of an Indigoid-Producing Strain, Pseudomonas sp. PI1. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00622-15. [PMID: 26067966 PMCID: PMC4463530 DOI: 10.1128/genomea.00622-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas sp. strain PI1 can cometabolize indole in the presence of phenol to produce various indigoids. Here, we present a 7.2-Mb draft genome sequence of strain PI1, which may provide insight into the study of phenol-indole cometabolism and its application in aromatic bioremediation and wastewater treatment processes.
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Wang J, Zhang X, Fan J, Zhang Z, Ma Q, Peng X. Indigoids Biosynthesis from Indole by Two Phenol-Degrading Strains, Pseudomonas sp. PI1 and Acinetobacter sp. PI2. Appl Biochem Biotechnol 2015; 176:1263-76. [DOI: 10.1007/s12010-015-1644-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
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Genome Sequence of an Efficient Indole-Degrading Bacterium, Cupriavidus sp. Strain IDO, with Potential Polyhydroxyalkanoate Production Applications. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00102-15. [PMID: 25767238 PMCID: PMC4357760 DOI: 10.1128/genomea.00102-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cupriavidus sp. strain IDO has been shown to efficiently transform indole, and the genus of Cupriavidus has been described as a promising cell factory for polyhydroxyalkanoate synthesis from low-cost wastes. Here, we report the draft genome sequence of strain IDO, which may provide useful genetic information on indole metabolism and polyhydroxyalkanoate production.
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Qu Y, Zhang Z, Ma Q, Shen E, Shen W, Wang J, Cong L, Li D, Liu Z, Li H, Zhou J. Biotransformation of indole and its derivatives by a newly isolated Enterobacter sp. M9Z. Appl Biochem Biotechnol 2015; 175:3468-78. [PMID: 25725798 DOI: 10.1007/s12010-015-1518-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 01/21/2015] [Indexed: 11/25/2022]
Abstract
In this study, a novel bacterial strain M9Z with the ability of producing indigoids from indole and its derivatives was isolated from activated sludge and identified as Enterobacter sp. according to 16S ribosomal RNA (rRNA) sequence analysis. UV-vis spectrometry and high-performance liquid chromatography-mass spectrometry analysis indicated that the products produced from indole, 5-methylindole, 7-methylindole, and 5-methoxyindole were indigo with different substituent groups, and the possible biotransformation pathways of indole derivatives, i.e., indole(s)-cis-indole-2,3-dihydrodiol(s)-indoxyl(s)-indigoids, were proposed. The conditions of indole transformation and indigo biosynthesis by strain M9Z were optimized, and the maximal indigo yield (68.1 mg/L) was obtained when using 150 mg/L indole, 200 mg/L naphthalene, and 5 g/L yeast extract. The transformation rates of 5-methylindole, 7-methylindole, and 5-methoxyindole by strain M9Z were all close to 100 % under certain conditions, making strain M9Z an efficient indigoid producer. This is the first study of indole biotransformation and indigoid biosynthesis by genus Enterobacter.
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Affiliation(s)
- Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China,
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16
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Rajeswari P, Jose PA, Amiya R, Jebakumar SRD. Characterization of saltern based Streptomyces sp. and statistical media optimization for its improved antibacterial activity. Front Microbiol 2015; 5:753. [PMID: 25653640 PMCID: PMC4301002 DOI: 10.3389/fmicb.2014.00753] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 12/11/2014] [Indexed: 11/17/2022] Open
Abstract
A moderately halotolerant Streptomyces strain, designated JAJ13 was characterized and a culture medium was statistically optimized to improve its antibacterial activity. Based on the phenotypic and molecular characteristics, strain JAJ13 was identified as a moderately halotolerant Streptomyces sp. JAJ13. Novelty of the strain JAJ13 in production of antibacterial compound was assessed by sequence analysis of KSα gene and LC-MS analysis of the active compound. Optimization of the culture medium for antibacterial compound production by the strain JAJ13 was performed with statistical methodology based on experimental designs. Initially, a starch based basal production medium was selected out of eight different production media screened for antibacterial compound production by Streptomyces sp. JAJ13. Plackett-Burman design was employed to screen the influential media components affecting the antibacterial compound production. Subsequently, statistical optimization of selected medium components was performed by employing the response surface methodology (RSM) with Box-Behnken design. The optimum initial level of CuSO4.5H2O, (NH4)2SO4 and K2HPO4 for the highest antibacterial activity was determined to be at 4.45 mg, 1.96 g, and 1.15 g in 1 L of distilled H2O, respectively. PBD and RSM guided design of experiments resulted in a maximum antibacterial activity of 23.37 ± 2.08 mm, which is a 78.8% increase in comparison with that obtained in the unoptimized medium. This study points the success of statistical model in developing an optimized production media for enhanced antibacterial compound production by Streptomyces sp. JAJ13.
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Affiliation(s)
- Pandiyan Rajeswari
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University Madurai, India
| | - Polpass Arul Jose
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University Madurai, India
| | - Richa Amiya
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University Madurai, India
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17
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Shen P, Song Z, Zhang Z, Zeng H, Tang X, Jiang C, Li J, Wu B. Screening ofBurkholderiasp. WGB31 producing anisic acid from anethole and optimization of fermentation conditions. J Basic Microbiol 2014; 54:1251-7. [DOI: 10.1002/jobm.201400049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/11/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Peihong Shen
- College of Life Science and Technology of Guangxi University; Nanning Guangxi China
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics; Nanning Guangxi China
| | - Zhangyang Song
- College of Life Science and Technology of Guangxi University; Nanning Guangxi China
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics; Nanning Guangxi China
| | - Zhenyong Zhang
- College of Chemistry and Ecological Engineering; Guangxi University for Nationalities; Nanning China
| | - Huahe Zeng
- College of Life Science and Technology of Guangxi University; Nanning Guangxi China
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics; Nanning Guangxi China
| | - Xianlai Tang
- The Science and Technology Department of Guangxi; Nanning Guangxi China
| | - Chengjian Jiang
- College of Life Science and Technology of Guangxi University; Nanning Guangxi China
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics; Nanning Guangxi China
| | - Junfang Li
- College of Life Science and Technology of Guangxi University; Nanning Guangxi China
| | - Bo Wu
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics; Nanning Guangxi China
- College of Chemistry and Ecological Engineering; Guangxi University for Nationalities; Nanning China
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Formulation and Statistical Optimization of Culture Medium for Improved Production of Antimicrobial Compound by Streptomyces sp. JAJ06. Int J Microbiol 2013; 2013:526260. [PMID: 24454383 PMCID: PMC3885193 DOI: 10.1155/2013/526260] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/02/2013] [Indexed: 12/30/2022] Open
Abstract
Streptomyces sp. JAJ06 is a seawater-dependent antibiotic producer, previously isolated and characterised from an Indian coastal solar saltern. This paper reports replacement of seawater with a defined salt formulation in production medium and subsequent statistical media optimization to ensure consistent as well as improved antibiotic production by Streptomyces sp. JAJ06. This strain was observed to be proficient to produce antibiotic compound with incorporation of chemically defined sodium-chloride-based salt formulation instead of seawater into the production medium. Plackett-Burman design experiment was applied, and three media constituents, starch, KBr, and CaCO3, were recognised to have significant effect on the antibiotic production of Streptomyces JAJ06 at their individual levels. Subsequently, Response surface methodology with Box-Behnken design was employed to optimize these influencing medium constituents for the improved antibiotic production of Streptomyces sp. JAJ06. A total of 17 experiments were conducted towards the construction of a quadratic model and a second-order polynomial equation. Optimum levels of medium constituents were obtained by analysis of the model and numerical optimization method. When the strain JAJ06 was cultivated in the optimized medium, the antibiotic activity was increased to 173.3 U/mL, 26.8% increase as compared to the original (136.7 U/mL). This study found a useful way to cultivate Streptomyces sp. JAJ06 for enhanced production of antibiotic compound.
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Genome sequence of a novel indigo-producing strain, Pseudomonas monteilii QM. J Bacteriol 2012; 194:4459-60. [PMID: 22843591 DOI: 10.1128/jb.00867-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas monteilii is a versatile bacterium found in various niches. A newly isolated strain, P. monteilii QM, can effectively produce indigoids from indoles. Here we present a 5.76-Mb assembly of the P. monteilii genome for the first time. It may provide abundant molecular information for the transformation of aromatics.
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