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Dolz M, Monterrey DT, Beltrán-Nogal A, Menés-Rubio A, Keser M, González-Pérez D, de Santos PG, Viña-González J, Alcalde M. The colors of peroxygenase activity: Colorimetric high-throughput screening assays for directed evolution. Methods Enzymol 2023; 693:73-109. [PMID: 37977739 DOI: 10.1016/bs.mie.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Fungal unspecific peroxygenases (UPOs) are arising as versatile biocatalysts for C-H oxyfunctionalization reactions. In recent years, several directed evolution studies have been conducted to design improved UPO variants. An essential part of this protein engineering strategy is the design of reliable colorimetric high-throughput screening (HTS) assays for mutant library exploration. Here, we present a palette of 12 colorimetric HTS assays along with their step-by-step protocols, which have been validated for directed UPO evolution campaigns. This array of colorimetric assays will pave the way for the discovery and design of new UPO variants.
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Affiliation(s)
- Mikel Dolz
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - Dianelis T Monterrey
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - Alejandro Beltrán-Nogal
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - Andrea Menés-Rubio
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - Merve Keser
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - David González-Pérez
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | | | - Javier Viña-González
- EvoEnzyme S.L., C/ Faraday 7. Parque Científico de Madrid, Cantoblanco, Madrid, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain.
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Deng JJ, Hu JY, Han XY, Li Y, Luo XC, Wang ZL, Li JZ. Degradation of indole via a two-component indole oxygenase system from Enterococcus hirae GDIAS-5. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131707. [PMID: 37379596 DOI: 10.1016/j.jhazmat.2023.131707] [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: 04/12/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Animal farming copiously generates indoles, which contribute to odor and pose a challenge for deodorization. While biodegradation is widely accepted, there is a lack of suitable indole-degrading bacteria for animal husbandry. In this study, we aimed to construct genetically engineered strains with indole-degrading abilities. Enterococcus hirae GDIAS-5 is a highly efficient indole-degrading bacterium, which functions via a monooxygenase YcnE presumably contributes to indole oxidation. However, the efficiency of engineered Escherichia coli expressing YcnE for indole degradation is lower than that of GDIAS-5. To improve its efficacy, the underlying indole-degradation mechanisms in GDIAS-5 were analyzed. An ido operon that responds to a two-component indole oxygenase system was identified. In vitro experiments showed that the reductase component of YcnE, YdgI, can improve the catalytic efficiency. The reconstruction of the two-component system in E. coli exhibited higher indole removal efficiency than GDIAS-5. Furthermore, isatin, the key intermediate metabolite in indole degradation, might be degraded via a novel isatin-acetaminophen-aminophenol pathway involving an amidase whose coding gene is located near the ido operon. The two-component anaerobic oxidation system, upstream degradation pathway, and engineering strains investigated in this study provide important insights into indole degradation metabolism and offer efficient resources for achieving bacterial odor elimination.
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Affiliation(s)
- Jun-Jin Deng
- Agro-Biological Gene Research Center, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangdong Academy of Agricultural Sciences, No. 20 Jinying Road, Tianhe, Guangzhou, Guangdong 510640, China; Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, The Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, No. 1 Dafeng Street, Wushan Road, Tianhe, Guangzhou, Guangdong 510640, China
| | - Jing-Yi Hu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou, Guangdong 510006, China
| | - Xue-Ying Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou, Guangdong 510006, China
| | - Yang Li
- Agro-Biological Gene Research Center, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangdong Academy of Agricultural Sciences, No. 20 Jinying Road, Tianhe, Guangzhou, Guangdong 510640, China
| | - Xiao-Chun Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou, Guangdong 510006, China
| | - Zhi-Lin Wang
- Agro-Biological Gene Research Center, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangdong Academy of Agricultural Sciences, No. 20 Jinying Road, Tianhe, Guangzhou, Guangdong 510640, China.
| | - Jia-Zhou Li
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, The Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, No. 1 Dafeng Street, Wushan Road, Tianhe, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture Heyuan Sub-center, Heyuan, Guangdong 517000, China.
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Regar RK, Singh D, Gaur VK, Thakur RS, Manickam N. Functional genomic analysis of an efficient indole degrading bacteria strain Alcaligenes faecalis IITR89 and its biodegradation characteristics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:51770-51781. [PMID: 36820967 DOI: 10.1007/s11356-023-25955-0] [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: 10/04/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Indole is a nitrogenous heterocyclic aromatic pollutant often detected in various environments. An efficient indole degrading bacterium strain IITR89 was isolated from River Cauvery, India, and identified as Alcaligenes faecalis subsp. phenolicus. The bacterium was found to degrade ~ 95% of 2.5 mM (293.75 mg/L) of indole within 18 h utilizing it as a sole carbon and energy source. Based on metabolite identification, the metabolic route of indole degradation is indole → (indoxyl) → isatin → (anthranilate) → salicylic acid → (catechol) → (Acetyl-CoA) → and further entering into TCA cycle. Genome sequencing of IITR89 revealed the presence of gene cluster dmpKLMNOP, encoding multicomponent phenol hydroxylase; andAbcd gene cluster, encoding anthranilate 1,2-dioxygenase ferredoxin subunit (andAb), anthranilate 1,2-dioxygenase large subunit (andAc), and anthranilate 1,2-dioxygenase small subunit (andAd); nahG, salicylate hydroxylase; catA, catechol 1,2-dioxygenase; catB, cis, cis-muconate cycloisomerase; and catC, muconolactone D-isomerase which play an active role in indole degradation. The findings strongly support the degradation potential of strain IITR89 and its possible application for indole biodegradation.
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Affiliation(s)
- Raj Kumar Regar
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- Drug Standardisation Unit, Dr. D.P. Rastogi Central Research Institute for Homoeopathy, Noida, 201301, Uttar Pradesh, India
| | - Deeksha Singh
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Vivek Kumar Gaur
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Ravindra Singh Thakur
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
- Analytical Chemistry Laboratory, Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Natesan Manickam
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India.
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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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Ma Q, Qu H, Meng N, Li S, Wang J, Liu S, Qu Y, Sun Y. Biodegradation of skatole by Burkholderia sp. IDO3 and its successful bioaugmentation in activated sludge systems. ENVIRONMENTAL RESEARCH 2020; 182:109123. [PMID: 32069749 DOI: 10.1016/j.envres.2020.109123] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Skatole is the key malodorous compound in livestock and poultry waste and wastewater with a low odor threshold. It not only causes serious nuisance to residents and workers, but also poses threat to the environment and human health due to its biotoxicity and recalcitrant nature. Biological treatment is an eco-friendly and cost-effective approach for skatole removal, while the bacterial resources are scarce. Herein, the Burkholderia strain was reported to efficiently degrade skatole for the first time. Results showed that strain IDO3 maintained high skatole-degrading performance under the conditions of pH 4.0-9.0, rotate speed 0-250 rpm, and temperature 30-35 °C. RNA-seq analysis indicated that skatole activated the oxidative phosphorylation and ATP production levels in strain IDO3. The oxidoreductase activity item which contained 373 differently expressed genes was significantly impacted by Gene Ontology analysis. Furthermore, the bioaugmentation experiment demonstrated that strain IDO3 could notably increase the removal of skatole in activated sludge systems. High-throughput 16S rRNA gene sequencing data indicated that the alpha-diversity and bacterial community tended to be stable in the bioaugmented group after 8 days operation. PICRUSt analysis indicated that xenobiotics biodegradation and metabolism, and membrane transport categories significantly increased, consistent with the improved skatole removal performance in the bioaugmented group. Burkholderia was survived and colonized to be the predominant population during the whole operation process (34.19-64.00%), confirming the feasibility of Burkholderia sp. IDO3 as the bioaugmentation agent in complex systems.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China.
| | - Hui Qu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shuzhen Li
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shengwei Liu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Yuanyuan Qu
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China.
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Ma Q, Zhang X, Qu Y. Biodegradation and Biotransformation of Indole: Advances and Perspectives. Front Microbiol 2018; 9:2625. [PMID: 30443243 PMCID: PMC6221969 DOI: 10.3389/fmicb.2018.02625] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Indole is long regarded as a typical N-heterocyclic aromatic pollutant in industrial and agricultural wastewater, and recently it has been identified as a versatile signaling molecule with wide environmental distributions. An exponentially growing number of researches have been reported on indole due to its significant roles in bacterial physiology, pathogenesis, animal behavior and human diseases. From the viewpoint of both environmental bioremediation and biological studies, the researches on metabolism and fates of indole are important to realize environmental treatment and illuminate its biological function. Indole can be produced from tryptophan by tryptophanase in many bacterial species. Meanwhile, various bacterial strains have obtained the ability to transform and degrade indole. The characteristics and pathways for indole degradation have been investigated for a century, and the functional genes for indole aerobic degradation have also been uncovered recently. Interestingly, many oxygenases have proven to be able to oxidize indole to indigo, and this historic and motivating case for biological applications has attracted intensive attention for decades. Herein, the bacteria, enzymes and pathways for indole production, biodegradation and biotransformation are systematically summarized, and the future researches on indole-microbe interactions are also prospected.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Food and Environment, Dalian University of Technology, Panjin, 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, China
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Zhang X, Qu Y, Ma Q, Li S, Dai C, Lian S, Zhou J. Performance and Microbial Community Analysis of Bioaugmented Activated Sludge System for Indigo Production from Indole. Appl Biochem Biotechnol 2018; 187:1437-1447. [DOI: 10.1007/s12010-018-2879-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/09/2018] [Indexed: 11/29/2022]
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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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Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole. PLoS One 2015; 10:e0125732. [PMID: 25928424 PMCID: PMC4416020 DOI: 10.1371/journal.pone.0125732] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/25/2015] [Indexed: 11/24/2022] Open
Abstract
Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.
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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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Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community. ISME JOURNAL 2014; 9:603-14. [PMID: 25191996 DOI: 10.1038/ismej.2014.161] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/21/2014] [Accepted: 07/27/2014] [Indexed: 11/09/2022]
Abstract
Although uncultured microorganisms have important roles in ecosystems, their ecophysiology in situ remains elusive owing to the difficulty of obtaining live cells from their natural habitats. In this study, we employed a novel magnetic nanoparticle-mediated isolation (MMI) method to recover metabolically active cells of a group of previously uncultured phenol degraders, Burkholderiales spp., from coking plant wastewater biosludge; five other culturable phenol degraders-Rhodococcus sp., Chryseobacterium sp. and three different Pseudomonas spp.-were also isolated from the same biosludge using traditional methods. The kinetics of phenol degradation by MMI-recovered cells (MRCs) was similar to that of the original sludge. Stable isotope probing (SIP) and pyrosequencing of the 16S rRNA from the 'heavy' DNA ((13)C-DNA) fractions indicated that Burkholderiales spp. were the key phenol degraders in situ in the biosludge, consistent with the results of MRCs. Single-cell Raman micro-spectroscopy was applied to probe individual bacteria in the MRCs obtained from the SIP experiment and showed that 79% of them were fully (13)C-labelled. Biolog assays on the MRCs revealed the impact of various carbon and nitrogen substrates on the efficiency of phenol degradation in the wastewater treatment plant biosludge. Specifically, hydroxylamine, a metabolite of ammonia oxidisation, but not nitrite, nitrate or ammonia, inhibited phenol degradation in the biosludge. Our results provided a novel insight into the occasional abrupt failure events that occur in the wastewater treatment plant. This study demonstrated that MMI is a powerful tool to recover live and functional cells in situ from a complex microbial community to enable further characterisation of their physiology.
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McClay K, Wan B, Wang Y, Cho S, Yu J, Santarsiero B, Mehboob S, Johnson M, Franzblau S, Steffan R. A novel combinatorial biocatalytic approach for producing antibacterial compounds effective against Mycobacterium tuberculosis (TB). Appl Microbiol Biotechnol 2013; 97:7151-63. [DOI: 10.1007/s00253-013-5012-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/18/2013] [Accepted: 05/20/2013] [Indexed: 11/30/2022]
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Shi S, Ma F, Sun T, Li A, Zhou J, Qu Y. Biotransformation of Chloro-Substituted Indoles to Indigoids by Phenol Hydroxylase from Arthrobacter sp. W1. Appl Biochem Biotechnol 2013; 170:951-61. [DOI: 10.1007/s12010-013-0234-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 04/09/2013] [Indexed: 11/29/2022]
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Shi S, Ma F, Sun T, Li A, Zhou J, Qu Y. Biotransformation of indole to indigo by the whole cells of phenol hydroxylase engineered strain in biphasic systems. Appl Biochem Biotechnol 2013; 169:1088-97. [PMID: 23306892 DOI: 10.1007/s12010-012-0069-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Accepted: 12/26/2012] [Indexed: 10/27/2022]
Abstract
Biotransformation of indole to indigo in liquid-liquid biphasic systems was performed in Escherichia coli cells expressing phenol hydroxylase. It was suggested that indole could inhibit the cell growth even at low concentration of 0.1 g/L. The critical Log P for strain PH_(IND) was about 5.0. Three different solvents, i.e., decane, dodecane, and dioctyl phthalate, were selected as organic phase in biphasic media. The results showed that dodecane gave the highest yield of indigo (176.4 mg/L), which was more than that of single phase (90.5 mg/L). The optimal conditions for biotransformation evaluated by response surface methodology were as follows: 540.26 mg/L of indole concentration, 42.27 % of organic phase ratio, and 200 r/min of stirrer speed; under these conditions, the maximal production of indigo was 243.51 mg/L. This study proved that the potential application of strain PH_(IND) in the biotransformation of indole to indigo using liquid-liquid biphasic systems.
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Affiliation(s)
- Shengnan Shi
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
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Qu Y, Shi S, Zhou H, Ma Q, Li X, Zhang X, Zhou J. Characterization of a novel phenol hydroxylase in indoles biotransformation from a strain Arthrobacter sp. W1 [corrected]. PLoS One 2012; 7:e44313. [PMID: 23028517 PMCID: PMC3441600 DOI: 10.1371/journal.pone.0044313] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/01/2012] [Indexed: 11/30/2022] Open
Abstract
Background Indigoids, as popular dyes, can be produced by microbial strains or enzymes catalysis. However, the new valuable products with their transformation mechanisms, especially inter-conversion among the intermediates and products have not been clearly identified yet. Therefore, it is necessary to investigate novel microbial catalytic processes for indigoids production systematically. Findings A phenol hydroxylase gene cluster (4,606 bp) from Arthrobacter sp. W1 (PHw1) was obtained. This cluster contains six components in the order of KLMNOP, which exhibit relatively low sequence identities (37–72%) with known genes. It was suggested that indole and all the tested indole derivatives except for 3-methylindole were transformed to various substituted indigoid pigments, and the predominant color products derived from indoles were identified by spectrum analysis. One new purple product from indole, 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one, should be proposed as the dimerization of isatin and 7-hydroxylindole at the C-2 and C-6 positions. Tunnel entrance and docking studies were used to predict the important amino acids for indoles biotransformation, which were further proved by site-directed mutagenesis. Conclusions/Significance We showed that the phenol hydroxylase from genus Arthrobacter could transform indoles to indigoids with new chemical compounds being produced. Our work should show high insights into understanding the mechanism of indigoids bio-production.
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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, China.
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Qu Y, Ma Q, Zhang X, Zhou H, Li X, Zhou J. Optimization of indigo production by a newly isolated Pseudomonas sp. QM. J Basic Microbiol 2012; 52:687-94. [PMID: 22359270 DOI: 10.1002/jobm.201100516] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 11/20/2011] [Indexed: 11/08/2022]
Abstract
Optimization of indigo production process from indole using a newly isolated phenol-degrading bacterial strain was performed by Plackett-Burman design and response surface methodology. The strain designated as QM was identified as Pseudomonas sp. according to 16S rDNA analysis. Spectrum analysis of indole biotransformation products revealed the presence of indigo and a by-product indirubin. To improve indigo yield, Plackett-Burman design was used to select significant factors from 8 viriables. Then response surface methodology based on a 2(3) central composite design was used to further optimize the transformation process. Under the optimal conditons, strain QM can produce 27.20 mg/l indigo after 24 h cultivation at 30 °C, which was 151.3% higher than that from the initial conversion condition. The results indicated that Pseudomonas sp. QM should be a potential candidate for indigo industial production.
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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, PR China.
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Santos PM, Sá-Correia I. Characterization of the unique organization and co-regulation of a gene cluster required for phenol and benzene catabolism in Pseudomonas sp. M1. J Biotechnol 2007; 131:371-8. [PMID: 17826858 DOI: 10.1016/j.jbiotec.2007.07.941] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 07/09/2007] [Accepted: 07/20/2007] [Indexed: 11/26/2022]
Abstract
This work describes a new genetic organization and co-regulation of a cluster of genes involved in the first steps of phenol and benzene catabolic pathways in Pseudomonas sp. M1, different from the established models for Pseudomonas upper pathway. Pseudomonas sp. M1 was isolated by others from the sediments of the Rhine River and exhibits an exceptional biodegradation ability towards a wide range of toxic and/or recalcitrant compounds. Although the taxonomic classification of strain M1 could not be determined, we found in a previous study that Pseudomonas citronellolis is the closest species. The genetic organization characterized in this study, the phc (phenol catabolism) genes, includes eight clustered genes, encoding a catechol 1,2-dioxygenase (phcA), a multicomponent phenol hydroxylase (phcKLMNOP) and the transcriptional regulator PhcR (phcR). PhcR controls the transcription of the referred seven clustered genes from two catabolic promoters: Pa (for phcA) and Pk (for phcKLMNOP). In agreement with in silico prediction, the activity of Pa and Pk promoters was proved to depend on the presence of sigma(54). Both promoters are phenol and benzene inducible and evidence supporting the unique sigma(54)-dependent co-regulation of the phenol/benzene inducible genes phcA and phcKLMNOP, mediated by PhcR, was obtained.
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Affiliation(s)
- Pedro M Santos
- IBB, Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av Rovisco Pais, 1049-001, Lisboa, Portugal
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